That sounds more like a clutch issue than the trans, maybe an issue engaging the plates. Especially if you are feeling it in the clutch pedal and not in the shift stack. I have had some funny things happen to me on the new 6MT that I never experienced in the e36 M3 5speed.
I attributed the engagement issues to the clutch delay valve not keeping up when I am power shifting and have only felt a slip due to engagement fault once, which was a bad one.
After a lot of miles, MT Bimmers have always been known to develop clutch rattle wich is noticeable in low gears and when cold but fades after a few miles of warm-up.