Just adding some updated notes on things I've tried and results:
The issue seems to happen when saving over a previous file. I've tested saving with Pokemon Green, Ruby, Sapphire, and Emerald all with the same result. I've loaded and used the identical games in an emulator to test if there are some issues with the roms but everything saves as expected from the emulator. I will be testing a new micro SD card shortly to see if that is the issue.