My teleport pad will sometimes keep teleporting me back onto the ship instead of down to the planet. Is there a solution for this issue?
The answer, unfortunately, is that there might not be anything you can do. Starbound is in early beta, so right now, it is going to have lots of bugs and is rather likely to crash.
What you can do is go to Starbound's forums to submit a bug report. Hopefully, the devs will address whatever is causing your problem soon.
In my experience this always happens if the target location has been removed (flag or teleporter was physically destroyed), but is still in bookmarks.
If that is the case, you'll have to walk to the location you want to visit.