All three of them did not practice all week, so this was expected. Especially for Gronkowski, whose recovery time has been well advertised. He won't be back until Week 16 at the earliest.
Chandler Jones was reported to have a "mild high ankle sprain" so it's possible that he could miss the Houston game as well. He has not practiced since injuring that ankle against the Colts.
Logan Mankins has been missing from both games and practice since he injured his nakle in the Bills game. He wasn't able to consistently get on the field before that either. It's not clear what the time table for his return is. Fortunately the Patriots offensive line have been able to survive without him. Yet, the Dolphins defense (T-10th in sacks) might be a good test to see how this line can hold up without him.
Key injuries aside, the Patriots are still good enough to beat the Dolphins Sunday.