In the most recent episode of Marvel's Agents of S.H.I.E.L.D., we learn that
Mack and Bobbi are working another incarnation of S.H.I.E.L.D., self-dubbed the “real” S.H.I.E.L.D.
The leaders of this group don’t like Coulson because
He’s following the same path as Nick Fury (non-transparent leadership) and he isn’t the same after he was injected with alien DNA.
That makes sense. But then I wonder, why don’t they officially remove Coulson from power after introducing themselves?
If they think that Coulson would resist such official order, they can always finish it hard way after that. I don't think Coulson's S.H.I.E.L.D. (which has financial problems) can stand a chance against real S.H.I.E.L.D. (which has a Helicarrier). Talking about Fury's cube, there's no point in searching Coulson's office with a toy car if you know the location. After crushing the band S.H.I.E.L.D., the room can always be searched in a better way. Why exactly is the real S.H.I.E.L.D. playing monkey?