Chris Bosh was on form to score 28 points and condemn the Bulls to defeat, with the visitors being held to 35% on shooting.
"There were several [shot-clock violations] in which it was good ball movement," Thibodeau told reporters.
"Then the ball was just held and you got to know what the clock is. We have some guys that aren't experienced.
"They're holding on to it when you got to get the ball up to the rim."
The loss sees the Bulls sitting in second place in the Central Division with a record of 29-26.