The Lester move proved to be an enormous factor.
You don't underestimate Jon Freakin' Lester.
Dodgers had lefty/right/right coming up. Game was 3-1 (how important was that fourth run?) and Lester simply wasn't pitching well (more line drives and fly balls, not many ground balls, third time through the order) for me to essentially forgo a chance at scoring a run. This has nothing to do with "underestimating" Jon Lester but everything to do with scoring a very important run.
The moves were not moves that were bad UNTIL THE PLAYERS didn't execute. Montgomery giving up a hit to a lefty. Strop walking Utley. Bryant not getting an out on the ground ball. These are all things that are not in Joe Maddon's control; he's put his players in a place to succeed and they didn't get it done. Chapman comes in and gets exactly what you need in that situation which is two strike outs. Ross didn't work any off-speed stuff in to Gonzalez so Gonzalez had plenty of opportunity to time a fastball (even 102) and he got a pitch in a good place to simply extend and shoot up the middle.
When I think a manager makes a mistake, I think he made the mistake before the outcome. I just don't see lifting Lester to drastically improve your chances of scoring and asking your bullpen to get 9 outs as a huge thing.