During the song "I'm Mean" Bluto picks up large chair. Three people standing by a window disperse to avoid being hit by the chair when Bluto turns to throw it out the window. We see Bluto throw the chair, but when the camera cuts back to the window it is not the chair but a small barrel that goes through the window.
During the scene in the Diner where Whimpy sits down at Popeyes table there are two ketchup bottles present. Each time the shot switches perspective, one of the bottles keeps going from half full to completely full.
The racing form that Wimpy puts back in his coat pocket winds up on the floor when Olive finds it and is later seen back in his hand (on the boat) while he's asking Sweet'pea about which horse to bet on.
After Poopdeck Pappy throws the can of spinach at Popeye and bonks him on the head, you can hear Swee-Pea laughing at it, but when it almost immediately cuts back to Pappy, Swee-Pea looks like he's about to cry, when he should've been still at least smiling.
The Paramount logo used at the opening was never used for any of the Paramount Popeye cartoons, though it is portrayed as being from a Popeye cartoon. Also, the opening credits sequence shown (doors of the wooden ship) was from the earlier Fleischer Studios cartoons, as opposed to the later Paramount cartoons.
As per the info in the trivia section of this film, the make up and appliances for Popeye's massive forearms were not ready. So in some scenes, especially the boxing match, if you look at the inside of his forearms, you can see that they are merely flesh colored pads tied over Robin Williams' arms (the strings are visible).