Unfortunately, I wasn't able to reproduce this issue, so it needs more information for investigation. I couldn't fix the bug until I'm able to repeat it.
If you experience it next time, please watch all the conditions carefully. Under Premoderation panel, premoderated Topics and Posts are stored under different sections, so it should be easy to keep this in mind in advance.
I've tried both cases on
miniBB demo, i.e. when a user makes similar two topics with the similar title and the similar message; and when a user posts the same message to a couple of existing topics. Both messages «arrived» to the Premoderation panel's different sections, and I've repeated the steps you've mentioned, i.e. approved one topic/message and rejected the other and removed the user from panel. This all worked like it should.
You also have to watch what you're doing carefully. It's quite possible you've just occasionally rejected both messages, in this case they will be both gone, for sure.