Pokemon GO glitch might leave your Pokemon stranded at a gym

Some Pokemon GO users are finding their Pokemon stuck at gyms. Once a user assigns a Pokemon to defend a gym, they seem to disappear. They don't appear at the gym, but if you try to use them for anything else, you get a message saying your Pokemon is defending a gym. Niantic seems to be aware of the issue, but they haven't detailed what's causing the problem, nor have they said when a fix is coming.