Surprise during implementation included;
No easy mirroring function in Unity, so many animations had to be mirrored manually by me.
Motionbuilder having a bug making animations appear locked in place when in fact when exported they were actually moving forward. This was solved when Motionbuilder was restarted.
Bones not part of the CAT rig suddenly losing all animation and going limp when trying to mirror animations in unity, another reason to manually mirror the animations in Motionbuilder.
In addition to this there were a bunch of different versions of the animation scripts floating around with only the programmers having the most current ones resulting in very old animation behavior being displayed during beta testing. I believe not being able to fully use sourcetree is mostly to blame for this.