As I said, in my quest log, only the "Warn Railroad about Bunker Hill" is checked, but after I speak to the courser to start the mission, the BOS shows up and he calls for backup, screwing over my plan completely.

Anyone else get this? any way to fix it? I've reloaded previous saves but this still happens!

All factions show up no matter what

I had this too, although i didnt inform anyone and BoS showed up and i got the dialogue with the Courser that implied i had informed them ("You're late"). BoS were not hostile to me either (even after killing most of them.

The end played out the same, Father was suspected i had informed them.

It also messed up the quest for me too, i couldn't relay the synths back to the institute and all they did is thank me for sparring them as soon as i interacted with them.

According to the wiki, both only show up if you inform both and the courser calls for backup. I only informed the RR so none of that should have happened.

bump

My first play through I only helped the institute and didn't inform BoS or RR yet both still showed. None were hostile to me either so I think it may just be a bug.