Well, you have 2 possible issues-
1) its probably a good idea to replace the trans fluid in the car- you can use the bmw fluid or you choose your redline or Royal purple fluid of choice.
2) it might be a good idea to replace/flush out all of the brake fluid in the car and make sure that the clutch line is bled VERY well. Sometimes, the hydraulic system in these cars can accumulate moisture over time and or, the fluid gets dirty- this can cause the clutch to not disengage properly which can create the notchy feeling you are getting.
Both of those things are super cheap to do and should be done first. It cant hurt!
Then, if that does not fix the issue, it could be the clutch. Worst case scenario, the transmission...
I replaced the trans in my 08 m3 at 5200 miles!!!! due to a bad 2nd gear syncro