While I was playing flood, I’ve seen Spartans labeled as enemies. When I killed one, I was booted for betrayal. Later, I was playing a game where I was last man, then shot by a flood Spartan with a pistol. Anyone?
Occasionally when a player joins a game that has already begun, the player will spawn with an Assault Rifle and Pistol. In the match they will be labeled as an enemy to both the Human and Flood sides. This glitch is usually fixed at the beginning of a new round.
-Hope this helps clear things up 
This exact same thing has happened to me before. And it’s not just when players join it gets glitchy, when they are killed and switch sides it happens too.