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.
While the babies are singing in the Reptar wagon in the river, Phil and Lil switch places between shots.
The propellers fall off of Stu's "Dactar" in one shot, but reappear later fixed back on when he finds the babies.
In the Rangers' station, the tuning dial on the radio disappears and then re-appears.
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.
During Stu and Grandpa Lou's pursuit to find the kids, for a few frames, Stu's car actually clips between the mattress truck and the oncoming tank truck when he goes to pass the mattress truck. Technically a collision would have taken place, thanks to Stu's reckless driving.
The babies' take on the word "hospital" is spelled as "hopsical" according to the synopsis on the back cover of the original 1999 VHS, but the closed-captioning spells it out as "hopsicle" (which rhymes with "Popsicle").
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.
After Tommy's baby brother Dil is born, he is brought home from the hospital after four weeks (roughly one month) without an explanation why he was in the hospital that long. Most babies are brought home from the hospital within 1-2 weeks unless they require more time of diagnosis.
For odd reasons, Didi's doctor Dr. Lipschitz assumed Dil whom she was pregnant with being a girl and that the nursery side of the room Tommy shares with the newborn was girl-themed - only to find out later at birth that Dil is in fact a boy and leading to the nursery being re-themed after all.
While the babies are lost in the woods, the baby bottle Tommy and Dil drink from is shown to be full every time either one drinks from it, but they don't have a milk carton or jug to refill it every time.
After the kids are rescuers by their folks, news anchor Rex Pester appears shows up with a black eye and a head bandage without an explanation of his injuries.
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.
Near the end of the song "This World Is Something New to Me", the newborn babies are shown urinating into the ceiling and forming a rainbow. Boys' and girls' body parts for urinating are private, so it would be very difficult for a girl to do it.
After Stu passes in front of the Nighty Night Mattress truck with the babies inside the trailer full of mattresses, the truck ends up spinning out of control and crashing into the barrier with the driver jumping out. Technically, Stu who's been driving recklessly the whole time is the one responsible for the accident but is nonetheless let off the hook.
The license plate to Stu's car has vanity plates with his name on it. Thanks to his reckless driving in a pursuit to find the kids, his actions would make it easier for other drivers to identify him by his name on his registration plates for his careless driving antics and that he could face legal consequences, including having his driver's license suspended and/or revoked - which he's nonetheless let off the hook.
In the baby delivery room where Didi gives birth to Dil, only she and Stu are the ones to not wear a hairnets. Patients and visitors, besides just doctors themselves are also required to wear hairnets for safety reasons in order to prevent loose hair from coming into contact with surgical instruments and areas of the body where surgical procedures are being done.