MTV News noticed that a couple of days ago, Grillo tweeted that the Cleveland production was wrapping up, and are working with the assumption that Grillo himself is done shooting for the film. They're also, based on another tweet, claiming that Grillo's character will be a S.H.I.E.L.D. Agent as well as being Crossbones--a narrative that fits some of what we've seen in terms of Nick Fury and S.H.I.E.L.D. being at odds.
To what extend it's because S.H.I.E.L.D. is actually evil versus just fallout from Fury's disobediance to the Council in The Avengers we don't know, of course--but Robert Redford, who plays a high-ranking S.H.I.E.L.D. official, has referred to himself as one of the film's villains.