I've come across a couple of issues in MegaMan Battle Network 4 and 5.
In 4 (Blue Moon), the game goes black after a battle or accessing the menu during WoodMan's scenario. The SneakRun subchip prevents battles from starting, but it expires too soon, and I can't go into the menu to access another one because that causes the game to black out. Saving the game also causes the game to go black, and reloading the game after saving also just plays the music but with a black screen i.e. can't do anything. I did make a save state before attempting to save, fearing that might happen, but when I reloaded it, I found that saving fails. So it seems there's no way to continue the game. I understand this problem happens on real gamepaks when played on a DS, but I'm not using a DS emulator to play it.
In 5 (Team Colonel, though this scenario is in both versions), I'm in the MineComp 4. I saved the game, and suddenly everything froze. Music still plays, but I can't move, access the menu, or anything. I tried reloading but it freezes after a second or two, so whatever's causing it triggered before I saved. I have no save state, but even if I did I bet it would have the same saving problem as 4.
Emulator I was using is a version of VisualBoyAdvance-M with a 2015 copyright date (downloaded in June), so it shouldn't be too out of date.
MMBN5 save file: MMBN5save.zip