The CWAL Rubber Room
Like, the whole reason old Will is keeping his father in the future is because when he was Young Will, his father never came back from the future and he didn't want to lose him again. Think about that for a second.
Also the robot. Young Will started repairing the robot and got as far as building it a new head, but then they just brought the finished robot back with them from the future, so I guess Will never finishes rebuilding the robot, or they have two of them?
I dunno, these things, and the third Ninja Turtles movie, used to drive me nuts when I was younger.