It sounds like the instruments you have tracks set to in your midi don't correspond to Pokemon Emerald's instruments. What I mean by this is that you could have an instrument set to use Electric Piano 1, which is instrument number 4 (counting 0), however instrument 4 in Pokemon Emerald is a square wave 2, for example. There isn't necessarily anything creating any sort of major error, you just need to change the instruments used by the tracks so that they align with the ones used in Emerald.
There's a post in research and development titled "a document on fire red voice groups and the instruments they play" that has a database of all the voice groups in Pokemon Fire Red, which includes the offset of each voice group as well as the name and number of the instrument (note that the voice group offsets probably aren't the same for Emerald). If you really wanted to insert your song into Emerald, then you could rip the voice groups from the game using a program called GBA mus ripper. Using it, you can get a sound font (sf2) for a particular voice group used in Emerald (or any other game that uses the sappy sound engine). You can then open the soundfont in a program called Viena to be able to listen to the samples in the voice group. Additionally, you can open midis in Viena, allowing you to listen to how your song will sound prior to compiling the midi in sappy. You need to know the offset of the voice group you want to rip to use GBA mus ripper. You can obtain this from sappy by double clicking on the hex number next to "Voices", which will open a dialogue where you can copy the offset. (By the way, if you do end up using GBA mus ripper, you need to use the "sound_font_ripper" executable in particular, I just didn't refer to it as such for simplicity)
