Hey,
Have this bug too, wrote at the start of 2.0 beta branch a bug report detailed, how this bug can be reproduced and also with screenshot what is happening (also with code examples). I really do not know if they are still working on the issue or can not reproduce it.
At the moment of 2.0.7 i have still this bug (no mods, clean world, clean installation with clean %appdata%/avorion folder, and can not fix that myself. Easiest way is to restart the server. The captian command "supply factories" is causing the bug. If he delivered goods to the destinantion the origin station losing free cargo space somehow. Has to be something with the sector simulation i think. So in short, no. you have to restart the server or not use the supply factories command.