The assistant might not have seen that the ball had rebounded off a United player, and this is where the referee and him should have acted as a team. It must have been clear to Dean that Ibrahimovic was well offside and a quick conference would have soon sorted it out.
Regarding the red card, yes, both feet were off the ground but he pulled out at the last minute and tucked his lower legs backwards. His fault was to get there just before Jones who had his leg extended with his studs showing. You could argue that it should have been a yellow card for Jones.