To me, there were two big decisions that should be 100% up to the manager and that Farrell got completely wrong
1) Blake Swihart should have been the starting catcher from day 1 of the season, which would have preempted the fateful move to LF. Given that there was no hit to organizational depth regardless of where Vazquez and Swihart played this season, the manager should have the final say here. Farrell chose the wrong guy. Leon had a great 5 weeks and almost bailed him out, but he turned into a pumpkin for the playoffs, when it mattered most. If Swihart had hit to his second half BABip-adjusted numbers this season, that would have been steady production out of the bottom of the lineup, instead of the 5 weeks of great production and 31 weeks of black hole.
2. Joe Kelly pitched more innings in relief for Pawtucket than he did for the Red Sox. I do not think the organization had veto power over whether Kelly was a starter or a reliever. We now know his future is as a relief pitcher. Farrell should have known this in March, and acted accordingly. Failing that, he should have known that by August 1st, but it appears that Farrell thought Barnes (who had options) and Hembree (who had options) were superior to Kelly. He was wrong, and admitted as much with his ALDS usage.
Earlier deployment of Kelly to the bullpen or consistent usage of Swihart at C easily could have been the 2 games needed to get home field in round 1. And who knows from there.