If the theatre in question is the Frozen theatre where the wheelchair seating is towards the front, I have some thoughts on that.
First off, lets say Row One is for Wheelchairs, and Row Two is for their families. Row Three might be reserved for a combination of both Wheelchair families and VIPs.
Now, let's say that we start filling the theatre and all the little Frozen Freaks, I mean Fans, want to sit up close as possible. However they have to sit in Row Four. How come? Because the first three rows are reserved for Wheelchair guests and VIP seating. No big deal, most people are fairly understanding when it comes to giving priority seating in a theatre to Wheelchairs and VIPs. So the Frozen Fans go to Row Four and find that they actually have a great view because the rows in front of them are barely half full. They sit for about fifteen to twenty minutes, they got there early, and the show begins.
Let's say we put those people standing in the back in row three. Now those families in Row Four are missing part of the show because people who got there after they did are filling in the row in front of them, while the show is in progress, blocking their view and taking forever to find a seat. The theatre is dark, there are distractions, and now someone falls, or drops their phone in Row Three. Those folks who showed up early are now stuck behind the folks who didn't care enough to be their on time to get a seat in the first place and are now taking forever to sit down because little Joey doesn't want to sit next to his father. (This really happens.)
Another explanation might be that if Row Three is for VIPs, then they need to keep that row free for those who enter after the show has already started.
It could also be that Disney has a strict rule about moving guests around after the show has started and the theatre is dark. You get one person who trips and injures themselves in a dark theatre, and now you have to call the paramedics and possibly cancel the show, which will tick off a boatload of people.
So in conclusion, Disney is very rarely "stupid" when it comes to operational choices like this and there are always a slew of circumstances that affect what the course of action will be.