Im on the last quest of the college of wintherhold and when i use the staff of magnus arcano isnt losing hes shield, i dont know if this is beacus of mods or if its a bug in the game, ive already done it with my main, but that was a long time ago, and i dont remember if it happened then and if i dealt with it in one way or another. but anyway my question is can mods affect the last quest of the college?

You want the Spoilers forum, but the short answer is yes. Mods can affect any aspect of the game.

But it's easy to check. Disable all your mods and try again.