Yeah, the Nate stuff is uncomfortable for sure - I was really glad we got a break from it last ep, actually! I can't blame Ted for it though? I don't think Nate's shown that Roy joining the staff affected him negatively at all, although he was taken aback on the pitch during Rainbow? The Will stuff has been happening since he started, for example, and the Colin bullying goes back to S1 too- see the snide little digs he keeps getting in (Never been blown: Is that why Colin is sad?)? In fact, I think that it's a deep seated issue that has to do with how his own dad never gives him any praise or recognition. He even called Rebecca a shrew last season, when he thought he'd been replaced for a hot second! So I think he lashes out when he feels small.
As for the bullying - Ted and Beard are aware, just like how they were aware of Nate getting bullied last season and were trying to get Roy to act. Beard has now intervened, and it's veeeeery obvious that Ted and Nate have not had any one on one scenes at all this season, and it's sooo telling that Nate's first concern was "Did you tell Ted?" when Beard did. So that Ted Talk (hehe) is coming, IMO!