thinner confirm damage.... 
unless you use hobby thinner? 

mr hobby leveling thinner also damage, this is depand on how the mixture ratio u apply.
So, when u failed to paint the color, it was really hard for u to remove the paint without the thinner...except u sand it.

Nail remover still can damage the thin part of the plastic, if:

u leave the liquid in the surface too long, or u putting too much liquid on it.

For paneling line, u can try to use eraser.

you sure you put right position or upside down? 

i think its the other way round did u check properly or not