when i finish a level the grade animation shows up but i'm pretty sure that durning that animation the timer stops but when i finish a level it doesn't stop, do i have to stop it manualy or what?

If you mean LiveSplit doesn't stop, for this game LiveSplit is not required, since we use In-Game timer for verifying runs.

try right clicking livesplit, then going to Compare Against and making sure it's set to Game Time. Also make sure you have the autosplitter turned on in the Edit splits menu. If those don't make it work then idk