According to the Diccionario panhispánico de dudas, the verb encontrar, used with the meaning of "finding someone or something unexpectedly or by chance", can be used in two ways:
- As the usual transitive verb:
Alguien llamó a la puerta. Abrió y encontró a Ángela.
- Or most frequently, as an intransitive, pronominal verb followed by the con preposition:
Alguien llamó a la puerta. Abrió y se encontró con Ángela.
So as you may now see, the verb in your example is used in this second way:
Un funcionario se encontró con que el dispositivo no funcionaba.
If used in the first way, the sentence would be like this (and also valid):
Un funcionario encontró que el dispositivo no funcionaba.