Sony is the compnay that makes the Spider-man films and Warner Brothers is the company that makes Batman.
I don't see why it should be a problem though, Matt, Harry Potter and Spider-man sets were being made at the same time.
Xwingyoda, Mega Bloks have got a license with Marvel (which they might not have by 2007 anyway, which is when Spider-man 3 comes out). So LEGO should still be able to have a licence with Sony to make Spider-man 3 sets.