I don’t know if I’d use bondo, that’s a plastic putty, isn’t it?
One way I just thought of which I haven’t used myself but can’t see why it wouldn’t work is to cover the plexi (where the gap is) in plastic cling film, the type to cover food with and then use a wood putty or filler to fill the hole. Then remove the plexi carefully when it’s dry.
Worst case is the cling film will stick to the filler but most likely it would just peel straight off. You could try it first on a bit of scrap to be sure.
Second way could be to build up a bit of filler around the place you messed up, wait till it dries, then use a sander and/or dremel to slowly sand back till the plexi fits in perfectly.