I don't really buy into any of the league-wide conspiracy theories where the refs are intentionally screwing the Celtics out of home court advantage.
However, I do think that there have been some tremendously bad calls this year, that have directly contributed to losses. The Lakers game where the refs fouled out KG, for instance, for a touch foul, after ignoring him getting repeatedly hacked two seconds before hand. That was poor refereeing, and looked pretty questionable at the time.
Lastly, as an aside, I don't think it generally makes sense to focus on free throw differential as a sign of good or bad officiating. If one team takes 50 jump shots, and another team takes 50 shots from in the paint, one would expect the second team to get to the line more. Even that's not completely reliable, because it's very possible for a team to shoot a bunch of inside shots without being fouled. I think the focus needs to be on individual bad calls, especially in the context of the flow of the game.