I just had a Game where the buttons were all mix up again. It even put grenade on the left trigger.Same here, i had one game where at the start even if i have bumper jumper selected , buttons were not in that configuration.
I've had this several times as well - I think it's to do with the way the game syncs profile data.
Even though your controller settings are saved locally, your controller settings are also saved to your gamer profile and synced online as well, and I suspect Halo 5 checks this online profile setting when you play in matchmaking, and if there's a delay in the sync then it sets a default scheme until the sync is complete.
Given most people play at home on their own Xbox's more often than not, I don't know why the online controller scheme is checked before the local one. Probably Microsoft just making strange design choices while on too much caffeine.