Just saw some highlights - looks like in the extended run in there were some narrow roads and there was a crash caused by the riders being very tightly bunched at the front. It split the peloton and Romain Bardet was one of the losers. Also explains why EBH, Thor and some other sprinters weren't involved at the end.
Indeed, after the fall the peloton was broken up in about 4 pieces. The first group waited a bit, so that 1 group could get back
(I believe Costa was actually signaling Giant to take it a bit slow so that this could happen)
however the other 2 groups (who joined each other) couldn't make it back anymore with the speed ramping up for the sprint
I guess this effectively makes Betancurt the appointed leader for Ag2r (Bardet losing time), Stetina for BMC (Cummings losing time and Tejay dropping out), Ion Izaguirre for Movistar (Gadret losing time - even faster than I had expected-), Simon Yates? for Orica (Gerrans and Albasini losing time) and Bob Jungels for Trek (both Schleck lost time)