I've never had issues with run mode turning off. Every time you load up the game run mode is off, but once you turn it on it always stays on for the rest of the session.
As for annoying glitches, if you are holding a direction when you respawn, the game doesn't register it and you get stuck. You can't move in that direction you're holding until you let go of the thumbstick and push it forward again. It's not a big deal if you're just playing the game normally, but when you're trying to speedrun it's a pain in the ass.
Also, this isn't really a glitch but it's very annoying how the save system doesn't start working until 15 seconds have passed. If you die in the first 15 seconds you respawn with all your weapons gone and reset health. If you forgot to save your game manually, you're screwed.
They're relatively minor problems though. I still love the game
