Continuity mistake: When Ash & co. are in the boat with Team Rocket (who's dressed as Vikings), watch Brock's shirt sleeve (The one away from Misty) when Misty puts Togepi inside her knapsack. It goes from a dark orange to green (the same color as Brock's vest) for a few frames before turning back.
Factual error: When New Island's reflection is in a window on Giovanni's helicopter, it is not reversed. (00:15:19)
Continuity mistake: When Officer Jenny speaks after Fergus puts his right foot forward, the clothes and accessories of some people change. (00:31:08)
Continuity mistake: When Ash says, "Wow!" the bowl of fruit changes as well as a cup changing from being on right of it to the left of it. (00:40:25)
Continuity mistake: When first showing a closeup of Ash, a plate next to the centre of the table goes from present to absent. (00:21:19)
Continuity mistake: When Misty retrieves the white card, the marks on Ash's cheeks go from present to absent. (00:27:35)
Revealing mistake: When Mewtwo is first seen in a tower, its right hand and the upper half of a woman's body are translucent with the screen showing through them. (00:25:56)
Revealing mistake: When Misty is setting the table, Brock's left foot clips through his cooking tool. (00:10:30)
Continuity mistake: When Mewtwo says that they stood as equals, Giovanni's right hand is five centimetres away from the nearest pole to the left of him, but in the next shot, it is one centimetre away. (00:08:20)
Suggested correction: As explained in the DVD commentary, Team Rocket don't know everything about Pokemon. They thought it was an Alakazam though.