First, when you're working with ASM, always make backups. Obsessively make backups.
What Jambo is saying is that, what has likely happened is that you "added" to the ROM. When pasting a line of code into a ROM, always make sure you do what is known as a "Paste Write", and not a "Paste Insert". The difference is that Paste Write overwrites what's there (and, if you are pasting in, it should be free space, so it doesn't matter if it is overwritten). Paste Insert, on the other hand, keeps what is there, but shifts it down, creating alignment issues (and, I believe emulators and GBAs can't read ROMs that are lengthened in this way).
I would say, check how long your assembled code is, and go in and delete that many bytes of free space after your code. That should fix it. And I do really mean "delete" - your hex editor will likely alert you that you're changing the size of the ROM, but your Paste Write already made the ROM larger, so you're just putting it back to its regular size.