I played a lot, but I never seen something like that.
Have you tried to play with video options ?
Or sometimes could also be the graphic card driver that changes something, if it's the case, a driver update or resetting it to default options should help.
Anyway this game really needs some polish... it's full of bugs/gliches... I could use pages to list them all... luckily I never found game-breaker issues, and there's always a way to go around them.
As an example, if the captain of an enemy ship is unreachable, you can just exit the game, continue, and teleport again to that ship... everything will stay as you left it, but the captain will be there too.
When this happens, the captain seems only visible in the ship map, not as a dot, but as a full 3D model over the ship, with the size of half a module.