I'm having a problem that may or may not be related. I have two ships now that I've used and modified over a number of games and then, at some point while in the garage, something showed up as broken integrity and the warning would not clear, but there didn't appear to be any red parts. No amount of adding and removing parts or creating and fixing broken integrity removed the warning or shows me any red parts to remove. I've flown through the ships, and in the case of the cruiser, built a copy of it ... and then had this come up again later during a subsequent modification.
In the process of taking these screenshots, it occurred to me that it was in the process of removing and re-adding the stickers on the Destroyer that the warning appeared. So I went to remove them just to be sure, and the piece of tetra armor in front of them lost its paint color and showed up with a red outline. Removing and re-adding the part finally cleared the warning.
I still don't know which piece is bugged in my Cruiser. X [
Edit: Hrmm, so the problem with the Cruiser was another tetra, in a similar spot on the left "hip". Which I'd placed mirrored with the one on the opposite side, naturally, but it was just the one. Hrng.