Other mistake: At the beginning, when one bad guy is sitting on a bench with a newspaper, we can read the date October 21, 1959 at the top. But, we also read Nov 3 1970 on the same page, under the mugshot of the Boss being released from jail. (00:04:20)
Other mistake: In the scene that Callaghan's daughter went into the portal, there is a track for the capsule to go into the first portal, but there was no track for the return portal.
Other mistake: The size of Dave's sub is too small for all the rooms it contains especially the cargo hold with hundreds of penguins and cages.
Other mistake: When Mr. Peabody is fencing with Robespierre in the sewer, the sword goes flying up and causes the manhole cover to go flying up too. But then the manhole cover falls through the opening to land on Robespierre. There's no way a round manhole cover can fall through its own opening.
Other mistake: Zarina creates orange pixie dust that is supposed to give you light bending powers. But when Zarina throws the dust on the fairies and they change powers, Rosetta ends up with orange which gives her animal powers, not light bending powers.
Other mistake: When Bill and Ben are pushing Thomas clear of the avalanche, they are not releasing any steam from their funnels.