When Harkspur, Sr., Littlejohn and Belenson visit Larry at his home to discuss the land deal, at one point he walks over toward the window and the other three men follow him; as they stop and continue their conversation, Harkspur can be seen holding his hat in his left hand. There is a jump cut to the next shot and Harkspur is now holding his hat in his right hand.
When Larry hits Duke, the cigar in Duke's mouth disappears.
When Larry Wilson returns home to a crowd, the name on the warehouse reads "Consolidated", but is reversed, thus showing that the negative was reversed.
When Larry goes on a hike with the Habersville rangers (essentially, the Boy Scouts) he gets winded. But if Larry has been involved with the Habersville rangers all along, then he would be in shape, whether or not he can remember anything about Habersville.
In the first scene of the movie when they're aboard ship, it is established that it is the 'last night out' and they would be docking in New York the next day. After falling overboard and being hit on the head with the oar, Larry's nine year amnesia is cured and in his conversation with Doc Ryan, reveals he believes it to still be 1931 and his last memory is having a fight on a train. Yet when they arrive in New York and he sees Kay, he remarks "eighteen days alone on a boat is certainly a long time to be alone on a boat for eighteen days". Given previous established events, he should have no knowledge of the full eighteen day boat trip and neither should he have had any feelings about one.