I'm guessing this has something to do with the framerate cap being much higher than the original game (original version probably ran at around 30fps or something). But the game was running fine at 1920x1080-144hz and then spazzed out randomly and all of the enemies were at super speed, this could have happened after I picked up the Spiritual Invincibility powerup, which slows all the enemies down, and then when it ran out they were all at super speed rather than normal speed, but I could be wrong and it could have just happened around that time coincidentally.

Has anyone found a fix for this? Restarting the game and loading from my save after it had happened, hasn't seem to have changed anything.

EDIT: I should add that I also changed the difficulty to Hardcore and then Hard around the same time from Normal, since Normal was way too easy, then I guess the huge increase in game speed is intentional when upping the difficulty? I really don't remember it acting this way when I played it on the N64 on higher difficulties. The higher difficulties probably do raise the game speed to up the difficulty but I feel like the enemies zipping across the screen is not intended and is probably an accident with them being made way too fast.