So if I got a game over screen, I press A and enter and Im still holing the A button, I cant press the enter button on the title screen. Yes Im still holding A and test it on other Emu and it works.

Just use another emulator

works for me on nestopia. Not sure why you're having the issue.

I think the A button not corporate with the Start button. Like seriously when I'm holding the A button, I can't click/execute the start button. I'm using Nestopia 1.40 maybe updating it will work now?

Might be that your keyboard is made in such a way that the A and Enter keys cannot be registered at the same time by whatever processes your inputs. This is known as "jamming," you can read more about it on the Wikipedia page for Rollover at https://en.wikipedia.org/wiki/Rollover_(key)

I don't use enter key on everything that wasn't important. I might check if OBS and LiveSplits have the ENTER key on it's hotkeys. I'm using Apvkp key shower if not this will probably cause it too. But even I don't open this program or not running in memory, it still not works even I'm not running those programs.

Just use FCEUX, that is another accepted emulator.

It's not the emulator, I have the exact same issue, but only on certain roms
When I use the "Super Mario Bros. (World)" rom, it just does not work
However, if I use the "Super Mario Bros. + Duck Hunt" it works

I don't know why it doesn't work unfortunately

I might test and use the SMB+Duck hunt+WCTM rom. I don't want to use FCEUX because of the enormous lag when recording/streaming.