Spike's collar reappears in multiple shots, even though it was ripped off by the wolf.
When Chuckie breaks his glasses, they switch back from broken to fixed.
Dil breaks the waist strap on Tommy's diaper at one point, but it appears fixed in later shots.
While the babies are singing in the Reptar wagon in the river, Phil and Lil switch places between shots.
After Tommy falls into the mud, his clothes alternate between being muddy and clean.
When the babies run into Boris's goat and the goat bleats, Boris responds "He's saying 'hello'!" The goat, however, is female, as she sports a prominent udder, and Boris and Minka brought her as a baby shower gift in order to supply goat's milk.
The newborn baby during the "This World is Something New to Me" segment that says "I can barely hear myself suck" has a full set of baby teeth grown in.
In the shot when Phil uses the lever to release a life preserver for Chuckie while the Reptar wagon is in "Aqua Reptar" mode while in the river, the lever is in the back seat when it should be on the control panel in the front.
Near the end while Tommy is shouting at Dill. His voice is heard but Dill's mouth moves.
On the plane, we see the goat inside the crate. There is no way it would have made it onto the plane, as the X-Ray scanners at Airport Security would have detected it.
The voice recordings to the Reptar wagon that toy inventor Stu Pickles constructed earlier in the movie are based on what Stu would say regarding Reptar. One of them says "Hang on to your diapies, babies" that only Tommy said in his Indiana Jones-style imagination. Stu would have never had that kind of phrase on the list of what "Reptar" says when the babies operate the Reptar wagon.