It isn't necessarily a tractor problem. One of 2 things, on many Deeres for a long time, the E pto causes the pto to start and stop abruptly, It doesn't modulate on slowly or wind down (PTO) when disengaged. Therefore when putting a cutter on a Deere, it is always recommended to go w/ a slip clutch.
The second possibility is what you are cutting or trying to cut. It doesn't take a lot to shear a pin. Maybe raise it up some to get off ground more.