I have noticed it but I think what he is doing is within the acceptable and basically this happens every sprint stage. I think he may be boxing a little bit more this year because he hasn't really shown in the sprints thus far that he can win them. So other lead out riders and sprinters give him less space than usual. That is also one of the reasons he's been below par in many sprint finishes - most notably stage 7 where he should have won 9 out of 10 times.
As for the Green jersey battle, I can see him gaining points back on Bennett in the coming week simply because he is a lot more versatile than Bennett. However, this might not matter since many intermediate sprints are positioned early in the stages favourizing Bennett.
He obviously would have finished higher up on stage 7 if his chain hadn't dropped.
Bennett will be able to contest all the remaining intermediates except 13 (and Sagan may not make that one unless he's in the break), so Sagan will have to try to contest the finishes on stages 12 and 14 (while Bennett sits in the gruppetto) to make up ground.
Stage 19 only has 1 categorized climb, but it has a very lumpy profile, and my recollection of visiting the area is that the roads do go up and down a lot. It's definitely a day for the break (mountains the 3 days before, TT the next day), so the question will be if a) Sagan can get in the break and b) Bennett can get in there with him and hold on to the finish.
It really looks like the green may be in question up to the Champs, which would be fantastic.