I have been learning and speedrunning this game the last 3-4 days, and I have a question if lag in this game is normal? Sometimes, you hit the button but it's like your input does not register if an enemy is shooting or lots of things going on in the screen. I know that most retro games are like that, and I understand it but when there is only a few enemies in the screen, game doesn't want to register the buttons you press. It's so frustrating! Is it normal? I'm playing on the original Genesis using RT5X on a CRT not a monitor.

Unfortunately, it is perfectly normal and there's nothing that you can do about it. Most levels don't have enough lag to cause a problem, but others -- like 5-5 -- can be brutal. Trying to kick that last ninja before the final boss door is like a 50/50 chance. Mashing the ninjitsu attack is a solid backup to save your life in the case of a knockback, but of course, it does take a few seconds. Also, you can change your route a little to compensate. For example, on 5-4, I jump over the final three red ninjas instead of kicking them because I don't trust the game to read my attack input.

Yeah, this is a game of eaten inputs and lag. Once you get a bit more comfortable with the run you'll identify problem areas and workarounds if they exist. The earthquake in 1-2 is laggy and can eat inputs as an example, but near the end of the stage if you move about an extra 10'ish pixels to the right before jumping up to the top ledge you can pretty much eliminate the eaten jump input. On the other hand, like quarbit pointed out, there are other places in the game where you're at the mercy of the game. The last part of stage 5-5 is probably the best example of that.