You don't have to worry, it is not necessarily flirting at all. Actually, it all depends on the intonation. You must pay more attention to the attitude, rather than the words.
It is usual in Spanish to answer with a compliment at the end, when you say thank you. You can hear:
- Gracias, guapa. (Beautiful)
- Gracias, maja (friendly)
- Gracias cariño (my dear. This is usual in shops, when salespeople thank you for your purchase)
Of course you can also hear just a description, like:
- Gracias, chica (girl)
- Gracias, muchacha (same)
This is not necessarily frequent, but you can hear it sometimes. It happens when the person wants to thank you and be friendly. Some foreigners use to find it too strong for the first time, but it's not weird here.
So, basically, it is just a compliment that reinforces the "thank you" part, with the expectation that you get happier to hear it too, so that we're two people happy now.
But of course, intonation matters. As I said at the beginning, the attitude can change the meaning of the whole sentence. However, I think it was probably "cute".