Hello. I hope some users here can answer some questions I have. :3
There's a hack for Mega Man 3 called "Mega Man 3 Improvement" which is made by kuja killer and can be found here: https://www.romhacking.net/hacks/992/
This hack has some issues running on Mesen. It has several bugs believed to be because of IRQ issues. A friend of mine messaged kuja killer, but he/she replied and said it was Mesen's fault. Said that it runs fine on hardware, though I don't know what was done to test this. But he/she could not diagnose Mesen due to being unable to run Mesen on his/her computer.
I wrote on Mesen's github about the problems, but users there said it was the hack's fault. Said loaders like the Everdrive aren't necessarily reliable for testing. See here: https://github.com/SourMesen/Mesen/issues/630
I know Mesen isn't in development anymore. But I was hoping some users of this forum can finally settle the matter. I'll describe the bugs below.
First: Mega Man 3 Improvement fixes the infamous glitched line on the stage select screen. Unfortunately, this causes the line's previous location to act strange in Mesen. It will cause the screen to jiggle at that scanline. Very easy to notice. It doesn't always happen, though. It sometimes does and sometimes doesn't at random. But usually it jiggles.
Second: This one is only seen (as far as I can tell) if you toggle the advanced setting "Enable PPU $2006 scroll glitch emulation" to on. Mesen doesn't recommend this, but I think it's more accurate to real hardware? Anyway, with this option on, enter a stage (let's say Hard Man) and pause the game. This brings up the weapon select menu. The menu will likely glitch out. Sometimes a lot of garbage data will appear in the menu, flashing on and off. Looks like some letters and numbers flashing.
Thank you for reading through this message, even if you don't have any answers for me. If you have any questions for me, please don't hesitate to ask.