Same problem here and it can also occur when changing characters which is what I was doing. Got in, made a romulan and the opened my Legacy Pack and now can't get back in to create my Reman.
Saucer separation was originally conceived in the TOS era as a life boat mechanism, not a combat option. However it evolved during the TNG thru Voyager era into a combat option so at this point they should be better than a shuttle in a fight, not worse.