I have a 99 Honda Civic and pulled the speakers out to install power door locks. I noticed it had some decent looking 6.5"s in it, but they are too big and the mounting holes are I would say maybe half inch off (out further) than the OEM holes. The speaker won't sit flush because the basket is too large. It says right on the bottom of the speaker 6.5". The baffle/basket is even large enough it covers the clip hole for the grill.

I know the stock speakers are 6.5", but is that 6.5" baffle not driver?

 

Oh the outside baffle across is 7.5"

 

Ah, previous owner just had oversized 6.5's. Yeah, 6.5 refers to driver.

it is possible previous owner just didn't have holes in the right places, if I read this correctly, and made his own. You could cut some of the door panel to force them to fit, or replace with some standard 6.5's from elsewhere.