Ok so I've beaten the main story siding with the minute men. I got the ending where all three factions (MM, RR, & BOS) are still alive as I haven't turned the BOS hostile. The only issue I have now is the BOS seems to attack my settlements yet they ARE NOT hostile to me specifically. They just attack my settlers but not me. Is this to try and make me shoot them so they become hostile or just a bug/glitch?

Seems to me it is a bug. I've never experienced BoS becoming hostile to any of the settlements. Though, there may be one explanation.

Have you completed quests for Proctor Teagan?