this has been a problem ever since the guild ship was introduced. The UI seems to be allowing for guild ship members, but when there are no guild crews and some of the local crew's btns extend into the guild ship area, the buttons and their special ability btns cannot be clicked; usually the two btns on the right end (I have 9 crew types in my launch bar). You have to drag the btns to the left before they accept clicks. This is extremely inconvenient in the heat of battle. Please fix it.
I recommend contacting support from the in-game help settings. It will give them your info automatically. Then you just have to describe the issue. It would help all the right people know about the issue