as a manned gun dweeb, I'm not sure it's a feature or a bug. I actually have not seen it lately. but I have seen it.
the workaround is just move to a same style base (small/med/large/v/port), click on the gun you want, then come back to the base with the crater in the indestructible and click H . or become a true jedi gun dweeb, and know where to click even when it's obscured