When the team has to share rooms these are the pairs and why

Steve and Bucky
They're the only ones strong enough to hold the other one down when they wake up screaming and they have been best friends since the forty's

Clint and Natasha
Clint is the only one who knows Natasha's story and is the only one Natasha let's touch her when she wakes up from a nightmare and she talks in Russian while crying and only Clint and Bucky understand Russian, Natasha is the only one who knows about everything that has happened to Clint so she knows what to say to comfort him

Bruce and Tony
Bruce knows how hard it must have been for Tony to almost die more than once so when Tony wakes up from a nightmare Bruce just starts talking science with him, Tony knows that Bruce doesn't like the hulk and has nightmares about him so when Bruce wakes up from one, he tells Bruce how hulk has done more than just destroy things or talks to him about science

Thor
Thor sleeps alone most of the time but when Loki comes with them as a consultant he shares with Loki and if either of them wake up from a nightmare they seek comfort from the other