If the mechanic took the car to fix the engine light, charged $3500 and he didn't fix it then definitely bring it back and make a scene. If it's running great now maybe the engine light is due to a separate issue. Is he telling you what codes it's throwing up? Ask for the actual code number. Perhaps it was throwing a code before the fix and now it's another code? Any codes on the paperwork?
Anyway, at least the engine is running great but I would be hassling him about the engine light coming on. After spending that much money you'd expect it to all be ok. Leave it a few days and then go back and say you're really disappointed after spending so much money and feel the problem isn't fixed and that you can't drive around with the engine light on so can he please look at it again and fix it. Don't be rude or angry, it will get you nowhere.