UPDATE: Thank you, everyone for the help and a big thank you to packability for the fix. In case anyone was wondering, I got this error when I saved in the lab in Phalox and after looking around this seems to be a common bug. If this happens to you download these files here and download lunar ips to apply the patch.
Don't use mGBA, while it is fantastic for GBA emulation it's GB/GBC emulation is not very accurate at all as it is in very early stages. Use either http://bgb.bircd.org/ or https://sourceforge.net/projects/gambatte/
If you want to help out, feel free to inspect the code and document the protocol for us. You can find Pokémon Crystal's disassembled source code on https://github.com/pret/pokecrystal. (Prism's source code is bundled in the .rar with every version, but the link code is the same as Crystal's, and the latter is likely to be at least slightly better documented.)
The main issue is that we simply don't understand the protocol the games use. The hardware protocol is documented in the Pan Docs quite well (http://bgb.bircd.org/pandocs.htm), but that's a simple serial byte protocol; the issue is the software protocol (layer 7, if you want) that is overlaid upon it. The code is a mess and we frankly don't have the time to go through it thoroughly until we figure it out.
Any help will be appreciated.
We strongly advice against using Visual Boy Advance. It's a bad emulator, it's inaccurate, and you will run into problems when using it to play Prism, since it is a very demanding game from a hardware point of view.
My best recommendation is to use BGB. (Right-click on the emulator window to access the menu.)
It was a bug in mGBA that I reported few days ago and it was fixed since.
Go to https://mgba.io/downloads.html , scroll down to development builds, and get that.
There still is a bug that causes savestates to revert the RTC to when the savestate was taken, so maybe wait until that is fixed too.
Hello! When I try downloading the patch, it gives me an error. Is something up or am I doing it wrong?
EDIT: Got it through this link.