- Fridge Logic: Why, exactly, does BabyCo need a secret lab beneath the city? Aside from the obvious question of how a child care company has the resources to make such a thing, from what we see they aren't doing anything illegal. Their testing methods appear to amount to monitoring the kids in controlled environments and deciphering what they're doing, otherwise they could just use the children of company employees and ask them to live at the office to keep the kids contained. There's no reason to treat their methods as some sort of secret conspiracy.
- Nightmare Fuel: The animatronic mascots. Including a Monster Clown with a tray of wind-up dentures, and a monstrous giant shaped like a baby, with the voice of Satan himself.
- Retroactive Recognition: Justin Chatwin in Baby Geniuses 2.
- Sequelitis: Why was a sequel made in the first place?
- Lots of shitty movies get even shittier sequels! But this!?
- And a third movie came out, with a fourth (and possibly even fifth) movie in the works!
- Special Effects Failure: The special effects are terrible. First, there's the method of making the babies' antics look convincing, by poorly Photoshopping baby faces over the bodies of little people (especially obvious during the dance scene), in addition to the disturbing SynchroVox-esque process used to superimpose CGI lipsync onto the babies faces. Also, one scene in which Sly backflips several times in front of the parents of his identical twin brother, you can easily tell it's a little person stuntman because of the height difference.
- Took The Bad Film Seriously: Jon Voight in the sequel. He's the only one not delivering his lines in monotone and attempted to make his character actually expressive.
- Uncanny Valley: The CGI used to make the babies' mouths move. It seems to have been lifted wholesale from Clutch Cargo.
- Don't forget the animatronic baby!