If you have your radar set to the whole system (press "R" to toggle radar modes) then all ships show up as red dots. Otherwise, friendly ships show up as blue arrows and enemy ships show up as red arrows.
Cloaking isn't implemented (so don't buy tachyon scanners
) so if there really is an invisible ship then it's probably a bug or your video memory contents getting corrupted.
You say you were fired on by a friendly base? That means one of three things:
1. You fired on a friendly ship.
2. You are carrying illegal cargo. (Demon Eggs, most types of bombs, strength enhancers, and anything else that sounds illegal
)
3. He was aiming at an enemy that was past you and you moved into the way of his shots.
Does any of this help?