What were your Manager's settings? If you had the bullpen setting turned to mildly aggressive or aggressive, they would pull him.
This setting would be used with a good pitcher to allow him to be brought back on fewer days of rest.
Sometimes some of the settings default back when you set up the game if you're not careful.
If you had your settings at the middle or towards conservative for Clemens OR if you had him selcted as an ACE, I don't think this should have happened.
Doesn't mean the gremlins in the game might not have done it to you.
I do get anomalous results from the robot every so often.

Dave N