I get that. Vaughn is having a terrific season, great vs LHP & more than acceptable vs righties. Rather than think Murphy is trying to throw games by sitting him I try to ascertain the thought process, which I think is something like this: He has settled into Lara & Frelick in RF because they're both much better OF gloves than Bauers, plus he's trying to keep Bauers healthy. That leaves the DH spot, and he still believes Yelich (at least vs RHP) is going to pay off. Has Yelichs' ABs been improving? I'd say yes; moderately. And when he reaches base he fits the baserunning pressure profile they love much more than Vaughn does. I think he also likes the idea of being able to bring Vaughn off the bench w/runners on base. Thing is, he needs to pull Yelich for Vaughn in certain situations & I don't know if that'll ever happen.
IMO his use of Vaughn makes sense up to a point, but I too would like to find more trips to the plate for him.