Night at the Museum/WMG

When a miniature "dies", they no longer can "come to life" at Sunset.
That's what would have happened in NaTM 2 if Octavus hadn't saved Jed from "dying". Yeah, he's a plastic miniature- but if he had "died" he just wouldn't ever have woken up after the museum "closed" (Sunset?) again.
 * Maybe Larry and co were worried about Jed in the hour-glass since once it's full, he would be stuck inside and could neither move or talk.

The paintings were actually portals to other universes.
This is why "Joey Motorola" could find a cell phone and "recreate" it while that is not historically accurate- it's because it's not our past, but a different plane of existance.

Ahkmenrah's death.
The Cain and Abel way: It's not outright stated that Kahmun killed his brother when "mother and father" gave Egypt to the more thoughtful Ahkmen, but considering that Ahkmen, who's the real thing, is still younger-looking then a model of his brother...
 * In the Wii video game, what Ahkmenrah said that his brother (Kahmunrah) may know more about the tablet after he died, which indicates that Ahkmenrah died before Kahmunrah.
 * This is also supported by the film. Kahmunrah states that his parents gave the throne to his younger brother, but he also claims that he was also a pharoh. The only way that both statements could be true is if he took the throne after Ahkmenrah's demise. And Kahmunrah doesn't seem to be someone patient enough to wait for natural causes to do his sibling in.

The figures are at least somewhat real when brought to life.
There was a scene in the sequel that brings special attention to Roosevelt's skin as it slowly morphs back to wax at sunrise. Also, the Civil War guys as well as the cowboys can fire bullets in the first one despite the fact that it's highly unlikely the museum would put working gunpowder in the replicas. The statues are able to talk, despite lacking lungs and a voicebox. And let's not forget the mummies, which proves the tablet can transform them to a certain degree, since it turns them from decayed corpse to a living person, and back again.

The fact that we saw the inside of a wax statue instead of guts when Roosevelt was run over does throw a monkey wrench into this theory somewhat. I guess the best explanation is that the transformation only goes in about skin deep.

Ahkmenrah is Marcos Al-Zacar from 24.
Yeah I know that this is either Jossed or just plain silly, but I want to tell this somewhere. You know that when. So maybe he was sucked by some black hole or some science phenomena that had to do with teleportation and was brainwashed. See, told you that was silly.

Dr. McPhee knew what was going on the whole time.
Personally, I don't believe this one, but somebody on IMDB suggested it. He gets angry at Larry because the museum is messy, but he never asks HOW it happened, he only tells Larry to do better next time or he's fired. Also, at the end, when McPhee has seen the news reports, he doesn't ask Larry HOW he could have created dinosaur tracks in the snow or put a caveman on the roof. And it would be sort of cool if the museum directors knew the secret and told their successors, just like the night guards.

McPhee has a crush on Larry.
At least in the sequel. He just seems... hurt (or something) that Larry left.

At some point, the tablet was displayed in England, either as part of a traveling exhibition or just on loan.
Ahkmenrah said he learned English when he was on display in Cambridge. He couldn't have overheard enough English to learn unless the tablet made him alive, so the tablet must have been with him. Since we're told the tablet was uncovered by archeologists working for the New York museum and brought back there shortly after, where it started to work its magic, he couldn't have been on display in Cambridge with the tablet before coming to New York. So, between the time the tablet was brought to New York and the trip to Cambridge, Ahkmenrah was awake in the museum, but didn't know English.
 * Except that Kahmunrah knew English, too, and French. Maybe they just absorb whatever's around them, even without the tablet, so they have the knowledge when it does bring them to life.
 * It was implied in the first movie that the exhibits still know what happens around them during the day, with the whole Dexter "A storm is coming" thing and Larry's thanks to Teddy, already a statue, at the end.