I think the only way you can completely stop that from happening is to play LIVE. If that is not an option, just hope that it doesn't happen too often.
Recently in a $100M theme league, Vida Blue had pitched 8 shutout innings, had a 1-2-3 8th inning, and had thrown 112 pitches. His TPC/MPC was set to 115/125, but Blue was removed for a relief pitcher to start the 9th inning. (There was no pinch hitter or double switch.) The reliever blew the lead, but the team won in 11 innings. But Blue did not get the win or the shutout. This was the third consecutive start that Blue was pulled after pitching 8 complete inninngs before he had reached his TPC (but the other 2 were not scoreless 8 IP). Another pitcher on the same team, Don Sutton, pitched a complete game loss, allowing 5 runs. Sutton threw 122 pitches, but his TPC/MPC was set to 110/120, and all RP were available. Go figure?
When I asked about these scenarios, I was told to play LIVE if I didn't like the SIM substitution decisions.