Basically agree with FB. Flat tire rolling the bike out to a customer does not mean top it off, it means investigate what the tune mechanic missed and fix it on the spot.
I don't quite understand how a brake pad could be loose enough to fall off and not be noticed during a tune, but I can imagine how it could be missed.
If you go back to the same shop, you give them an opportunity to make good on the situation. Maybe they swap tubes and fix the flat for free, offer apologies for the brake situation, which should horrify the service manager.
If you want to continue using that particular shop, confront them. If you'd rather not, you really don't gain much by going back and telling them about it. I'd still be compelled to write a short email note explaining things and see how it plays out, just for my own personal edification.