I scanned the entire Wiktionary database dump looking for nouns that didn't match the gender rules. This works by examining the wikitags of each noun and comparing it to the expected endings of l-o-n-e-r-s and d-ión-z-a, so it should be as accurate as the Wiktionary pages are. Nouns with dual tags like {mf} were skipped. The source code is available in my github as part of the WordTree package. After building the Spanish database with wordtree.py you can run gender.py to replicate these results: https://github.com/SurpriseDog/WordTree
Results
Of the top 7.7 thousand nouns, 3% did not follow the gender rules. I am limiting the search here to only nouns with a usage frequency greater than 1 fpm (frequency per million) in the OpenSubtitles frequency list to show a more accurate percentage of the nouns that are actually used.
For nouns ending in a, I found 2.5K nouns of which 1.7% were rogues. I am excluding nouns ending in -ma because there is no pattern. You have to memorize them as 39% of -ma nouns are masculine and 61% are feminine.
For nouns ending in o, I found 2.34K nouns of which 0.3% were rogues. In fact there were only 7 with a usage frequency greater than 1 fpm: La mano, foto, disco, seo, quimio, polio.
For nouns ending in e, I found 629 nouns of which 11% were rogues. Nouns ending in -dumbre like: La muchedumbre are always feminine.
Full List
Stack Exchange won't let me post the full list here because of character limits, so here is every word over 0.2 fpm. The strange 2 letter words are usually alphabetical letters like "La de" = the letter D. Wiktionary includes it, so that's why the program does too. Looking at the list, you will also notice a lot of loanwords here like El jazz or El yoga.
If you think a word shouldn't be included, (for example a profession like El poeta that could be masculine or feminine), check the associated Wiktionary page to see if there is an issue there that I am sourcing from here. In the case of El poeta, the feminine is sometimes La poetisa which is why they listed the noun as masculine.
FPM: Word: Gender:
34231 de m -> f
21603 la f -> m
7183 te m -> f
1942 he m -> f
1477 ese m -> f
935 día f -> m
925 noche m -> f
839 gente m -> f
666 madre m -> f
590 mujer m -> f
542 parte m -> f
470 razón m -> f
454 tarde m -> f
424 ve m -> f
332 contra f -> m
301 suerte m -> f
288 muerte m -> f
266 mano m -> f
245 clase m -> f
236 sangre m -> f
157 diez f -> m
153 calle m -> f
152 orden m -> f
135 frente m -> f
123 haz f -> m
117 mente m -> f
115 foto m -> f
107 hambre m -> f
106 normal m -> f
100 cualquiera f -> m
98 sal m -> f
97 cárcel m -> f
93 avión f -> m
91 nave m -> f
85 señal m -> f
83 carne m -> f
77 base m -> f
75 llave m -> f
74 especie m -> f
72 planeta f -> m
64 guardia f -> m
61 piel m -> f
55 fe m -> f
55 leche m -> f
53 camión f -> m
52 imagen m -> f
49 serie m -> f
44 central m -> f
40 fuente m -> f
38 dia f -> m
35 disco m -> f
34 mapa f -> m
34 nieve m -> f
33 clave m -> f
32 corriente m -> f
30 lord f -> m
28 miel m -> f
28 crisis m -> f
27 torre m -> f
26 medianoche m -> f
25 miss m -> f
24 superficie m -> f
24 madame m -> f
23 tele m -> f
23 fiebre m -> f
23 flor m -> f
22 moto m -> f
21 serpiente m -> f
21 frase m -> f
21 moral m -> f
20 arroz f -> m
20 costumbre m -> f
18 guión f -> m
16 fase m -> f
16 mediodía f -> m
15 miente m -> f
15 dosis m -> f
14 maíz f -> m
14 disfraz f -> m
14 bla f -> m
13 vodka f -> m
13 constante m -> f
12 pa f -> m
12 permanente m -> f
12 nube m -> f
12 be m -> f
12 marica f -> m
12 ave m -> f
11 lápiz f -> m
11 ataúd f -> m
11 cal m -> f
11 poeta f -> m
10 ajedrez f -> m
10 jazz f -> m
9.9 suite m -> f
9.6 gripe m -> f
9.6 postal m -> f
9.3 césped f -> m
9.3 inicial m -> f
9.1 récord f -> m
8.8 cometa f -> m
8.8 morgue m -> f
8.7 milord f -> m
8.6 sida f -> m
8.3 escriba f -> m
8.2 yoga f -> m
7.9 sobredosis m -> f
7.8 huésped f -> m
7.5 digital m -> f
7.4 cha f -> m
7.4 masacre m -> f
7.2 champaña f -> m
7.1 peste m -> f
6.8 tequila f -> m
6.5 profeta f -> m
6.5 anfitrión f -> m
6.3 sede m -> f
6.0 buda f -> m
6.0 gorila f -> m
5.9 labor m -> f
5.8 tos m -> f
5.5 spa f -> m
5.4 aprendiz f -> m
5.3 cumbre m -> f
5.3 barbie m -> f
5.1 tesis m -> f
5.0 record f -> m
5.0 seo m -> f
4.9 élite m -> f
4.9 che m -> f
4.9 catástrofe m -> f
4.7 labial m -> f
4.6 hipótesis m -> f
4.5 pirámide m -> f
4.4 circular m -> f
4.4 catedral m -> f
4.2 col m -> f
4.1 etcétera f -> m
3.8 diabetes m -> f
3.7 altavoz f -> m
3.7 golden m -> f
3.6 capataz f -> m
3.5 vacante m -> f
3.3 espiral m -> f
3.3 tranvía f -> m
3.2 escorpión f -> m
3.2 round f -> m
3.2 dote m -> f
3.1 violeta f -> m
3.1 pose m -> f
3.1 parálisis m -> f
3.0 higiene m -> f
3.0 patente m -> f
2.9 yakuza f -> m
2.9 metrópolis m -> f
2.9 fez f -> m
2.7 mugre m -> f
2.7 hipnosis m -> f
2.7 land f -> m
2.6 boulevard f -> m
2.6 tuberculosis m -> f
2.6 quimio m -> f
2.5 fa f -> m
2.5 abad f -> m
2.5 jerez f -> m
2.5 sucursal m -> f
2.5 elite m -> f
2.5 ye m -> f
2.4 pelvis m -> f
2.4 hepatitis m -> f
2.3 casanova f -> m
2.3 liebre m -> f
2.2 guion f -> m
2.2 génesis m -> f
2.2 sífilis m -> f
2.2 ale m -> f
2.2 incertidumbre m -> f
2.2 integral m -> f
2.2 nasal m -> f
2.1 psicosis m -> f
2.1 vocal m -> f
2.1 stand f -> m
2.1 hinchazón m -> f
2.0 artritis m -> f
2.0 podre m -> f
2.0 centinela f -> m
2.0 problemita f -> m
1.9 prótesis m -> f
1.9 muchedumbre m -> f
1.9 guardarropa f -> m
1.9 tanga f -> m
1.9 elle m -> f
1.9 ro m -> f
1.8 sor m -> f
1.7 diálisis m -> f
1.7 hélice m -> f
1.7 persa f -> m
1.7 gorrión f -> m
1.6 avestruz f -> m
1.6 nirvana f -> m
1.6 hold f -> m
1.6 cáliz f -> m
1.5 sien m -> f
1.5 res m -> f
1.5 ce m -> f
1.5 pe m -> f
1.5 chakra f -> m
1.4 sarampión f -> m
1.4 servidumbre m -> f
1.4 aeronave m -> f
1.4 variable m -> f
1.4 apendicitis m -> f
1.4 ingle m -> f
1.4 desliz f -> m
1.3 alcatraz f -> m
1.3 boutique m -> f
1.3 némesis m -> f
1.3 radial m -> f
1.3 meningitis m -> f
1.3 cloud f -> m
1.3 yugular m -> f
1.3 hijoputa f -> m
1.2 borgoña f -> m
1.2 vibrante m -> f
1.2 esclerosis m -> f
1.2 tapiz f -> m
1.2 quid f -> m
1.2 balboa f -> m
1.2 vigía f -> m
1.2 picazón m -> f
1.2 mantis m -> f
1.1 patriarca f -> m
1.1 compa f -> m
1.1 exmujer m -> f
1.1 mantra f -> m
1.1 neurosis m -> f
1.1 embrión f -> m
1.1 polio m -> f
1.1 underground f -> m
1.1 intemperie m -> f
1.1 regaliz f -> m
1.0 ge m -> f
1.0 mousse m -> f
1.0 squad f -> m
1.0 caries m -> f
1.0 lis m -> f
1.0 comezón m -> f
1.0 fondue m -> f
1.0 friend f -> m
1.0 druida f -> m
1.0 coliflor m -> f
1.0 psique m -> f
1.0 led f -> m
1.0 ardid f -> m
0.9 snowboard f -> m
0.9 centurión f -> m
0.9 chita f -> m
0.9 tata f -> m
0.9 estirpe m -> f
0.9 esfinge m -> f
0.9 credencial m -> f
0.9 vitro m -> f
0.9 mole m -> f
0.9 bilis m -> f
0.9 califa f -> m
0.9 insecticida f -> m
0.9 ébola f -> m
0.9 epidural m -> f
0.9 índole m -> f
0.9 rave m -> f
0.9 barniz f -> m
0.9 metamorfosis m -> f
0.9 ene m -> f
0.9 praxis m -> f
0.8 filial m -> f
0.8 laringe m -> f
0.8 cúspide m -> f
0.8 libido m -> f
0.8 bastión f -> m
0.8 problemilla f -> m
0.8 córdoba f -> m
0.8 performance m -> f
0.8 tweed f -> m
0.8 multinacional m -> f
0.8 marimacho m -> f
0.8 diócesis m -> f
0.8 variante m -> f
0.8 albornoz f -> m
0.8 fashion f -> m
0.8 koala f -> m
0.7 hache m -> f
0.7 diagonal m -> f
0.7 síntesis m -> f
0.7 armazón m -> f
0.7 estasis m -> f
0.7 nao m -> f
0.7 debacle m -> f
0.7 ere m -> f
0.7 tragaperras m -> f
0.7 metástasis m -> f
0.6 barbarie m -> f
0.6 semifinal m -> f
0.6 plebe m -> f
0.6 cirrosis m -> f
0.6 calvicie m -> f
0.6 apartheid f -> m
0.6 matiz f -> m
0.6 sinapsis m -> f
0.6 simba f -> m
0.6 encefalitis m -> f
0.6 pesticida f -> m
0.6 expo m -> f
0.6 bronquitis m -> f
0.6 uve m -> f
0.6 celulitis m -> f
0.6 podredumbre m -> f
0.6 fame m -> f
0.5 lumbre m -> f
0.5 conjuntivitis m -> f
0.5 fibrosis m -> f
0.5 trombosis m -> f
0.5 laúd f -> m
0.5 premiere m -> f
0.5 magenta f -> m
0.5 sinusitis m -> f
0.5 transversal m -> f
0.5 sepsis m -> f
0.5 quiz f -> m
0.5 ele m -> f
0.5 mediodia f -> m
0.5 efigie m -> f
0.5 falange m -> f
0.5 blitz f -> m
0.5 planicie m -> f
0.5 fedora f -> m
0.5 baguette m -> f
0.4 equis m -> f
0.4 astronave m -> f
0.4 maison m -> f
0.4 pardiez f -> m
0.4 manito m -> f
0.4 sintaxis m -> f
0.4 prole m -> f
0.4 necrosis m -> f
0.4 tragaluz f -> m
0.4 cortacésped f -> m
0.4 autómata f -> m
0.4 apa f -> m
0.4 terranova f -> m
0.4 intro m -> f
0.4 antifaz f -> m
0.4 taja f -> m
0.4 bocata f -> m
0.4 hidroavión f -> m
0.4 groupie m -> f
0.4 seño m -> f
0.4 gillette m -> f
0.4 mononucleosis m -> f
0.4 burka f -> m
0.4 hertz f -> m
0.4 catequesis m -> f
0.4 contraparte m -> f
0.4 laringitis m -> f
0.4 crin m -> f
0.4 acid f -> m
0.4 fotosíntesis m -> f
0.4 hermafrodita f -> m
0.4 chinche m -> f
0.4 mod f -> m
0.4 direccional m -> f
0.4 telequinesis m -> f
0.4 gouda f -> m
0.4 átame m -> f
0.4 simbiosis m -> f
0.4 aguamiel m -> f
0.4 miura f -> m
0.4 delicatessen m -> f
0.4 interfase m -> f
0.4 pastoral m -> f
0.4 laude m -> f
0.3 progenie m -> f
0.3 arquidiócesis m -> f
0.3 recortada f -> m
0.3 epidermis m -> f
0.3 beluga f -> m
0.3 psiquis m -> f
0.3 info m -> f
0.3 catarsis m -> f
0.3 comadre m -> f
0.3 marsala f -> m
0.3 escoliosis m -> f
0.3 anginas m -> f
0.3 ion f -> m
0.3 sinopsis m -> f
0.3 herbicida f -> m
0.3 tangente m -> f
0.3 furgo m -> f
0.3 mandala f -> m
0.3 anastomosis m -> f
0.3 kibutz f -> m
0.3 ratio m -> f
0.3 erre m -> f
0.3 estenosis m -> f
0.3 sud f -> m
0.3 notición f -> m
0.3 patronal m -> f
0.3 amniocentesis m -> f
0.3 osteoporosis m -> f
0.3 colitis m -> f
0.3 bacanal m -> f
0.3 esturión f -> m
0.3 eme m -> f
0.3 antítesis m -> f
0.3 gastritis m -> f
0.3 altamar m -> f
0.3 vedette m -> f
0.3 akita f -> m
0.3 gastroenteritis m -> f
0.3 raid f -> m
0.3 acrópolis m -> f
0.3 pancreatitis m -> f
0.2 offshore m -> f
0.2 password f -> m
0.2 nutella f -> m
0.2 andaluz f -> m
0.2 sazón m -> f
0.2 depre m -> f
0.2 contracorriente m -> f
0.2 endocarditis m -> f
0.2 hiel m -> f
0.2 troupe m -> f
0.2 sura f -> m
0.2 guardiamarina f -> m
0.2 amigdalitis m -> f
0.2 bocajarro m -> f
0.2 dermatitis m -> f
0.2 promo m -> f
0.2 desazón m -> f
0.2 peritonitis m -> f
0.2 euskera f -> m
0.2 kibbutz f -> m
0.2 segur m -> f
0.2 feta f -> m
0.2 archidiócesis m -> f
0.2 psoriasis m -> f
0.2 aluvión f -> m
0.2 ska f -> m
0.2 alud f -> m
0.2 halitosis m -> f
0.2 simiente m -> f
0.2 acidosis m -> f
0.2 efe m -> f
