Yes, it's called a bug!
Possibly, or maybe Ironclad couldnt get the AI to use the Z-axis so it cant make those jumps, so they added the z-axis movement so you could at least manually do it.
I only play large muti-star maps so maybe you have not found out the advantages of z-axis (though these strats are useless on single star maps)
Strat 1, I spilt my forces into 5 groups, 4 roving attacking groups and one defense group. The single defense group has to protect all my star systems, so it needs to be able to jump to other stars fast. I park that group high above a stars pole, advantage, almost no movement before it jumps to any star on the map, infact it almost always jumps without moving at all.
Strat 2, I always leave a scout parked at stars and to avoid them getting attacked I park them way up on the z-axis and nobody messes with them.