That part of the ROM seems to deal with the connections between each map, there are quite a lot of zeroes around there so I'm guessing that you overwrote the data there when trying to insert something (a map, script, tiles etc). A quick fix would be to make a back up of your ROM, open it in a HEX editor, goto (Ctrl+G) 0x486828 and replace what's written there with '0C 68 48 08'. That would be the very least you can do to make that error disappear, but it would be better to compare that section of your edited Emerald ROM to one that hasn't been modified in any way and then replace your edited data with what's there.
Since you're starting out I can understand that it could be a bit hard to do this, but its the simplest thing I can think of to remedy your problem.
When entering a double-battle in FR the game doesn't take two separate trainer images and pair them together, it uses a single image that has two people in it. You can see this is the case if you look at the images from 127 to 131 in Advance Trainer.
If you want to have two trainers appear when the trainer battle begins/ finishes you will have to do what GameFreak did and put them in the same sprite.