There was a strange behavior with altarian model 58 ship part, on a small ship, in a couple games. It appears oversized when placed, and then changes size when the placed piece is selected.
Another probably known bug is that part rotate sometimes fails to distinguish Y and Z axis (same rotation regardless of the dial you use).
Non-bugs are:
Animate rotation: Oscillate, the range on this scale should really be from -360 to 360, rather than -180 to 180, otherwise certain oscillations would be impossible to achieve.
I think it's not a bad idea to add a mirrored->added parts command. It saves the trouble of implementing a better handling of mirroring, for one. For another thing, having the mirror buttons grayed out is annoying. Being able to work with separate parts individually at need would be more flexible.
And there's no reason when a designer tries to delete, not to select the parts interfering with deletion - heck it even leads nicely into the "group selected parts" command, right?
I would also include a 'next hardpoint' keyboard command to supplement the traditional point-and-add method, because frankly it's hard to snag the one you want sometimes. This is the sort of polish that this game can't afford not to have, it being already 2015 and all!