First is undercutting. The shell appears to be cast with a line in it indicating where it's supposed to be trimmed. On my shell there was one corner where it was undercut and the line was still visible. So check if you have any of these issues and trim on the line. ( I could be wrong about the line as well, it could have just been something funky on my particular shell)
Second is general warping of the fiberglass. A little warping is acceptable as long as you can hold it flat by hand. To fix this you can clamp the shell down of a flat surface and heat it up with a heat gun and let it cool back down. Repeat as necessary. I'd also advise clamping it down like this to the motherboard when mounting it.
FYI don't melt your shell with the heatgun. If anyone melts their shell feel free to email GBFans on the weekends.
Thirdly is over-cutting. Your pic looks like over-cutting. I used bondo to fix this. Keep in mind anything within 1/4" is still perfectly accurate to the filming props. Mine wasn't really that large but it bothered me anyways.
There are other things you can do, maybe you have access to a giant belt sander? But this is what I did with this shell.
Here's a picture showing one of my clamps I used for heating/mounting/bondoing.
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