I noticed this doing a medical supply gathering mission in the Delta Volanis system. My officers will suddenly vanish never to reappear again. They'll (their dots anyway) then rubberband out and back to the spot they vanished. When the Nausicans arrive, they too are either under or in the terrain, or will attack invisibly and can't be fired back on.
There is also an issue at times when trying to distribute officer points. Raising an officer skill and clicking accept will update them properly, but seconds later will give an error message and reset, sometimes without returning the points.
Finally, a minor bug, when logging in, the Federation area and the Klingon area for characters to stand in will overlap into this odd mismash that usually vanishes when the character list loads.