NightDiveStudios. anyway, this looks more like maybe you are doing something wrong quest wise - have you checked some walkthroughs?
No I haven't and I'm sure it's a bug.
It doesn't say anything about limits in the manual and I've never encountered this problem before. It so far seems to only happen on the Flight Deck and I recently found out that it's just very picky bug wise; it recently let me have about 5 or so waypoints but no more, and player location and energy level seem to have nothing to do with it.
I also just use the GOG shortcut and the Steam shortcut I gave it.