Yes. He was less than 2 minutes away from losing the fight. I would call that trouble.
Also, using your head as punching bag on the ground isn't the best game plan. Regardless of your chin. You can't just sit there and hope that the next shot or shots aren't going to put you out. He was in trouble through the whole fight.
I know he was going to lose the fight, but was he really in trouble. Those shots sonnen was hitting all night really was not doing much damage. There was no point where Sonnen had a furry of GNP where the fight was going to be stop.
I know it isnt the best game plan but its anderson silva. He trains like that where guys actually do furry of GNP on him. He is also know to test his chin constantly in the RIvera fight. Also in the first fight once he got dropped he got right back up , dropped his hands to let sonnen hit him to show he can't be ko.