I was trying to do the beginner route to Tutorial 2 Skip, then I exited with the menu to go back to the main floor. Then for some reason I got to the upstairs part of the final stage while trying to do so. did anybody know about this? This can be found in the part where I arrive at eddy for the first shine.

This is a known thing that happens because the stage you are in does not reset upon the "quit game" button. It is banned on the leaderboard since it requires set up from a previous file and is also in the discord's faq. Btw if you wanna join the sm63 speedrunning discord, here's the link: https://discord.gg/c3q9pqn33s

If that same thing happened in an any% run would it be legal to continue if I go to bowser one

Should be as long as you don’t take advantage, but to avoid it, after you get a run to bowser 3, have another file that you can go to that can exit level. By exiting level, you get rid of the glitch.