When Joe buries the comic books in the past he does so at the base of a magnolia tree and also attached a sign to it. In the future when he recognizes the tree it has become a large post oak tree with the comic books buried at its base and the faded sign attached although at a higher altitude.
When Joe first learns that he is back in 1965 he says he was born in 1965. Then when he meets Lynyrd Skynyrd he says he was 8 years old when he heard about the plane crash that killed Ronnie Van Zant. This cant be so because Joe would've been 8 years old in 1973 and the plane crash that killed Ronnie Van Zant didn't take place until 1977. Also, in the first film, he said he was 11 years old in 1982, indicating he was born in 1971.
The name of the band Nazareth in the ending credits is incorrectly spelled as "Nazereth".
When Clem is about to have Joe Dirt whacked, Joe reveals the winners of 1977 Daytona 500. He decides to befriend Joe in hopes that his future predictions of the race winners are correct and true. Since Joe was mostly homeless his whole life, he wouldn't have been able to predict all those future NASCAR races.
When Joe goes to the bathroom on the plane, he gets stuck in the toilet. As he sits down the toilet makes a flushing-suction sound, but his hand never touches the button to flush.
Joe meets the Galinda on the bench in present day, then recalls his story. In this story he ends his journey and meets her (for the first time as the story is in his past), finding out that she is a guardian angel. He recognizes her as the woman on the bench, but as this was the first time he had met her, he should have recognized her at the start of the movie as the guardian angel from the past.