Those were, indeed, enemies. Battlegrounds like that have teams based on Grand Company. So there's one team for the Maelstrom (the red one), one for the Twin Adders (the yellow one), and one for the Immortal Flames (based on your description, that was your team). There's also a setting to get placed on a team at random regardless of your actual Grand Company affiliation (and this setting is always on when you join with a party rather than solo).

Can't really help offhand with the other questions.