I have finished the main story with The Minutemen, perfect outcome I have wanted - win with my army, yet save both The Railroad and Brotherhood of Steel.

But when I went to Railroad HQ to celebrate my victory with them, this is what happened:

Glory is completely ignoring me (when I press X to talk to her, I say "Glory" and she just stares as me, mute)

Desdemona is saying something like "I wish Glory was still with us" even though she stands just next to her!

PAM gives me a mission to clear the Brotherhood Patrol.

People are talking about defeating Brotherhood of Steel although that never happened.

That's the weird thing - The Railroad thinks that BoS has been destroyed and for some reason assume that Glory died. It's like I have skipped some important part in the game although I didn't.

I went to check The Prydwen to see if everyone from Brotherhood is okay. Everyone is fine, just complaining about how it should have been them instead of The Minutemen who destroyed the institute and not a single word about The Railroad.

TL;DR:

For some reason, The Railroad got bugged for me, thinking that Glory is dead and that we have defeated Brotherhood of Steel although we haven't and now they are giving me missions to clear BoS patrols although BoS is still friendly to me.