The incident happened around 16 and a half kilometres from the end of the 169.5km stage from Bourg d’Oisans, just a day after Team Sky’s Chris Froome faced abuse from some in the vast crowds on Alpe d’Huez.
The yellow flare seemed to be thrown over the heads of Team Sky’s riders, landing in the middle of the bunch with all the riders passing it safely.
Yellow jersey holder Geraint Thomas said he had not seen the incident. “I was fully in the zone then fighting for position. It was pretty stressful so I had no idea.”
The Welshman did, for a third straight day, hear boos as he collected his yellow jersey at the end of a stage won by world champion Peter Sagan. Asked why, he said: “I think that’s a question for the people out there. I don’t know. We just train hard, work hard and come here to try to win the race.”
The incident involving the flare came only hours after Tour director Christian Prudhomme called for calm at the roadside after events spilled over on Alpe d’Huez.
Froome was slapped by at least one fan and appeared to be spat at by another, before Vincenzo Nibali crashed after touching a spectator, with the 2014 Tour winner now out of the race due to his resulting injuries.
There had been fears about security on the mountain with Froome still facing lingering ill-feeling among some cycling fans following the salbutamol case in which he was cleared of wrong-doing just days before the Tour began.
Prudhomme said: “It was a very annoying climb of the Alpe d’Huez. The riders on the Tour, and champions of the Tour, must obviously be respected, as they are by the large majority of the public. I can only renew my appeals for calm, for common sense.”
Bora-Hansgrohe’s Sagan picked up his third stage win of this Tour as he overhauled UAE Team Emirates’ Alexander Kristoff and Arnaud Demare of Groupama-FDJ in the final few metres.