Could be a couple innocuous things; the clutch pedal needs to be dead down to the stops, a quarter inch will have you grinding the PTO gears. If you have the clutch down and try to engage the PTO too quickly, things are still spinning and will grind a touch too. I always press clutch & count... 1, 2, 3, then try the PTO lever.
Then there's the ever tricky 2 stage clutch. That one can fool you because you become used to the transmission gears changing in the top half of the clutch travel, but again the PTO only disengages at the bottom. You can tell when the mower spools up to speed long before the tractor starts to move when letting out the clutch. Still the same though, clutch fully down, engage PTO.
Oh, and I always engage the PTO at idle speed, then spool up to working RPM. Saves a lot of shock load.