My battery cavity filled with rain water due to a leak in my tail light of my 328i bmw wagon, and when my mechanic replaced the battery he said the new one was putting out too may amps and then fried the alternator. Is this really a thing?
The alternator puts amps into the battery, not the other way around... Unless he is talking about the voltage regulator, I guess you could blow that up but not really sure how likely that is in any shorting situation. Might have been a bad hookup attempt.
Is the alternator not working at all or is it just really really weak?
Its possible that having a dead battery caused your already worn out alternator to work harder full-time (a running car can continue to operate on just the alternator and no battery, although not electrically recommended) so that may have worn out the alternator during the (short) time you were running it like that.
If that happened, then more than likely you can just have the alternator rebuilt for much cheaper than buying another unit.
If the voltage regulator is blown, then depending on the car/alternator you can either replace just the regulator on the alternator, or you might have to replace the whole alternator, or you might have to replace the ECU.