Well if we're just going by hindsight, it would seem that drafting Giddens at #30 with the following centers still available (Pek at #31, DeAndre at #35, Asik at #36) was a pretty big blunder. Pekovic especially would look great in a C's uniform. Drafting Green in 05 with David Lee still available is pretty disappointing as well...but again, it's easy to pick out which players would be useful to us with the knowledge we already have, so I don't fault Ainge too much for these moves.
Other than that, I think his worst move was never getting a true back up for Rondo, instead relying on various point guards by committee - Marbury, Nate, House, Arroyo, West, Bradley, ect. It obviously wasn't very important in the playoffs where he played close to 40 minutes a night, but I do believe it led to the team relying on Rondo too much in the regular season. He also struck out pretty bad when it came to acquiring a legit big to back up KG, but at least he tried (Big Baby, Sheed, Shaq, JO, Erden, Krstic, Stiemsma, Wilcox, Darko...)