In some of my games when I go to modify a core ship design, I'll often end up with components on there that I haven't researched yet. For instance, I commonly have phasors stuck onto my Defenders when I first go to modify them. They don't seem to be taking up space and I can't re-add them once they're removed. I have yet to build one of these and try using it

Free phasors can't be all that bad.
This isn't a serious bug or a very annoying one, but a bug nonetheless.