A police officer pepper sprays a protester as another protester stands in front of the race director's vehicle during stage 16 of the Tour de France, a 218-kilometer ride from Carcassonne to Bagneres-de-Luchon.
According to Agence France-Presse, the bales of hay caused a stoppage about 16 miles into the stage's 135-mile route as farmers protested a decline in state aid.
In the bid to clear the road and detain the protesters police sprayed tear gas, which then drifted into the peloton and led to riders having to visit the medical auto to wash their eyes out.
A farmers' protest blocking the road.
Froome has been a repeated target of fans in this Tour after he was cleared of doping five days before the race began. Some reports stated police had used pepper spray, while others said it had been tear gas.
But the 25-year-old Lancastrian crashed with 6.5km to go, allowing Quick-Step Floors' Julian Alaphilippe to zip by and take his second stage win of this Tour.
"I'm a Francophile", he said.
Amid a general feeling of suspicion surrounding Sky and their sheer domination of the race, Froome has been spat at and manhandled, Thomas has been booed off the podium and some of Sky's staff have also faced abuse.
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Alaphilippe's excellent descending soon saw him pull out a big gap, and the current polka dot jersey holder stormed to his second stage win of this year's race.
It was Quintana's second career stage victory in the Tour, having also won a leg in 2013.
"I think he's got nearly a two-minute lead on Dumoulin, which I think is a pretty comfortable lot", Froome told reporters after finishing 1:35 behind stage 17 victor Nairo Quintana and 48 seconds behind Thomas.
Team Sky haven't made a statement about either incident at this point.
He may be the defending champion, but Froome will now be riding in service of Thomas for the rest of the Tour.
"I don't know how you prepare", Thomas says.
Thomas remained 1 minute, 39 seconds ahead of four-time champion Froome, with Dumoulin 1:50 back.
He picked up a handful of bonus seconds to go with the time gained on the road.
"This isn't how I wanted to finish my Tour and leaving it like this really hurts", Gilbert said.