Continuity mistake: After Obi-Wan's group has abseiled down the wall of the prison, two of the clone troopers in armour are carrying Separatist blasters instead of the Republic-issue blasters they had before and after. (00:09:38)
Continuity mistake: Besides Obi-Wan, Even Piell and Commander Cody, the exact number of people in Obi-Wan's group keeps changing.
Answer: I would say his death in Phantom Menace was more of a controversy. He was a fan favorite character from the movie, and his fight scene largely regarded as the best part of the movie. It was more he was brought back to please the Star Wars fans and few, if any, had problems with it.
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