When Xavier is talking to Magneto in the jail cell near the end, Prof. X calls Magneto "Ian", which is the name of the actor who plays Magneto, Ian McKellen. Chuckles galore!
He does, in fact, say "Indeed." Not only does it simply make more sense in the context of the conversation, but how likely would it be that a tremendous actor like Patrick Stewart would suddenly forget and call another actor by his real name and then dozens of crew members wouldn't catch it AND, on top of that, it would make it through post-production editing? This isn't a goof-up. Also, the same answer here applies to the urban legend about Mark Hamill yelling "Carrie!" at the end of Star Wars.