Here are some I noticed off the top of my head:
1) How is Reed able to stretch his regular clothing as well? Unstable Molocules.
2) If Sue is so worried about being in the lime-light then why have a wedding on a damn roof?
Where else would she have it? A Church that would be over ran by a crowd?
3) Where Willie Lumpkin?
...Who cares

He wasn't a major character in the first film.
4) We all know that Alicia is blind but can she not feel the force of the propellers coming at her? Even if she did feel the force wouldn't you be scared stiff if helocopter blades were coming towards you.
5) How did Doom get his costume passed the highly secured military base?
Again, its just a mask and armor, not weapons, plus he was helping the government and was trusted more than Reed.
6) Since Doom was 'cured', why would he even need to wear it?
...You really weren't paying attention were you? In the Castle scene his ancestors wore the Armor, you can clearly see them wearing the armor in one of the paintings.
7) I'm sure this isn't an error but the battle scene took place in China so why did they get married in Japan? Cause Japan is beautiful, and it obviously took place at least 2 days after the battle because Brian Poshen is there.