Though I've not had disappearing credits happen to me, I have had ships magically transferred when I change ships at a station. For instance, the other day I put my Cobra into storage at the Tavgi system, and dusted the cobwebs off my Asp. In both the storage location text and GalMap, my Cobra got described as stored in Ovimbiabas - and not in a station, oh noes, but in the star itself. Not the first time this have happened to me, so a little later I reloaded the game, and my Cobra got shown correctly as stored at Gordon Enterprise in the Tavgi system.
Methinks their little server database need some work. Either it receives so much data that it buffers it for later processing based on some kind of priority queue, so some changes takes a while to get corrected. Or the client need a fresh start to read some server database information.
In either case, it is a well known issue, and I assume the devs are working on it.