When I was testing my own emulator with Wario's Woods the mushrooms that you have to pick up/place wasn't rendering at all, also Mega Man 3 had problems with Gemini man level and most obvious was Jurassic Park which had many obvious glitches even at the loading screen.
The problem was that in mmc3 when writing to $E000 and $E001 it actually changes the internal cpu status register's flag and that is important because the irq does nothing if irq disable flag is set.
When I was testing my own emulator with Wario's Woods the mushrooms that you have to pick up/place wasn't rendering at all, also Mega Man 3 had problems with Gemini man level and most obvious was Jurassic Park which had many obvious glitches even at the loading screen.
The problem was that in mmc3 when writing to $E000 and $E001 it actually changes the internal cpu status register's flag and that is important because the irq does nothing if irq disable flag is set.
Source: https://www.nesdev.org/wiki/IRQ