Do you mean that there's some sort of bug associated with Z-axis movement, or do you consider it an exploit just because most of the game and ship movements normally function in a (roughly) 2d plane?
The two big examples I'd give are the starbase blindspot and minefield bypass.
Starbases have a known weapons blindspot directly above and below them. Position your units in these locations, and the starbase cannot attack them. The Vasari starbase is capable of moving, so it doesn't have this issue (it just turns upwards to face the threat) but you can defeat virtually any TEC or Advent starbase in this way. As well, targeting for security override protocol, mass disorientation, and meteor control is sketchy in the z-axis and often won't hit every target that it should.
The second issue is with minefields. By moving in the z-axis, you can go straight overtop of a minefield. The problem is, mines were balanced around 2D movement, and go from being sub-par to completely worthless if your opponent just goes over them. In theory they can be placed in 3D as well, but this limits your ability to fill out the gravity well and your opponent can now easily go around in 2D.
