Audio/visual unsynchronized: Littlefoot's lips don't move when he says "Cera, you came back!" while pushing the boulder on the Sharptooth.
Continuity: The scene in which the baby pterodactyls fight over the cherry uses two backgrounds, one for the vertical pan, another for the horizontal. The two backgrounds do not match exactly; particularly, the sky changes color, and a knothole in the bottom of the screen disappears and then reappears.
Continuity: In the scene where Ducky discovers Spike in his egg, Spike is portrayed as perhaps only two or three times the size of ducky. However, the next shot a few seconds later shows Spike coming out of the bushes at a size much larger than that. (6 or 7 times the size of Ducky, a state in which he remains throughout the rest of the movie)
Continuity: When Littlefoot and the gang settle to sleep on the sharptooth footprint, Cera joins them. She is next to Littlefoot, who is next to Spike. In the next shot, she is in-between Spike and Littlefoot.
Continuity: When Littlefoot and the gang run away from the sharptooth after their sleep, Petrie is on top of Littlefoot's head. After the rest of the gang run into the crevice, we see Littlefoot being chased and Petrie is not on his head. When Littlefoot does enter the crevice, Petrie is back on Littlefoot's head, but when the sharptooth breaks the crevice Petrie is not seen rolling down the hill with the gang. After the sharptooth is seen with its muzzle stuck in the now bigger crevice, Petrie reappears but in the next shot, both Petrie and Ducky are gone.
Continuity: Littlefoot's, Cera's and Spike's eye color changes from its normal color throughout various scenes during the movie then back again to its original color at least once each.