Lots of after market parts on an used car?

Question

what are some of the cons to buying an used car with lots of aftermarket parts

Answer 1

I assume you mean performance/modification parts?  Not simply replacing the alternator with a generic one, right?

Any manufacturer warranty may be voided.  If you buy an extended warranty, it too may be voided.

Aftermarket parts may or may not be correct for the application.  If they are mismatched, improperly installed, or low quality  you may be getting a lot of hidden damage.

Aftermarket parts may be an indicator of how the car was driven too.  If you see an inexperienced driver, and a lot of performance add-ons, its a safe assumption that it was not driven gingerly to church and back.