In Night At The Museum, the exhibits in the Museum of Natural History come to life and wreak havoc every evening. We see them causing extensive destruction on several different nights. However, sometimes this damage seems to be magically repaired, and goes unmentioned by the daytime staff of the museum, and on other occasions, the museum is left in a terrible state. Is there some explanation for this, or is it merely sloppy plotting?
There is nothing mentioned about how museum get cleaned every night after destruction but for the cleaning of destruction done in the end done by retired night guards.
Cecil, Gus, and Reginald are forced to become museum janitors to evade being sent to jail for their crimes. - (Source :Wikipedia)
The same confirmation has been provided on IMDb So who cleaned up the mess in the Museum lobby?