Something I've noticed with a couple ships is the odd positioning of their pivot points or essentially the ship's "0-0-0" position.
The two major offenders that come to mind are the NX class and the Ha'feh Assault Warbird.
The NX's pivot point is near the back of the ship between the nacelles. This makes the ship look as though it's turning faster than it actually is since the rotation axes aren't centered properly.
With the Ha'feh design, it appears that they've copied the hardpoint positions from the Haapax Warbird with it's separation ability. This places the pivot point on the very top of the ship. This also means the camera pivots around this point and doesn't give you a very good view around your ship with the camera being misplaced. In addition, when the ship turns it looks like it's hanging from a pendulum rather than rotating along the Z-axis while banking.
These are both minor nit-picks but should also be something easily fixed with a quick model adjustment.
Anybody know of any other ships with a similar issue?