The incidents have made some teams worry that fans are getting out of hand on the most famous climbs of the Tour.
After three gruelling stages in the Alps, the peloton enjoyed the closest thing to a day off as is possible in the middle of a Grand Tour on the relatively flat 167km trek from Bourg d'Oisans to Valence, and Team Sky delivered both Geraint Thomas and Chris Froome safely over the line to ensure there was no change to the general classification.
"It did worse than wind Merckx: It ruptured the fragile pact, the bond of trust that exists between the riders and the public", Bicycling.com's Richard Moore wrote in 2015.
Thomas won at the top of the iconic Alpe d'Huez on Thursday to tighten his grip on the race as Team Sky bid for a one-two finish in Paris.
The fans seemed to be directing most of their ire-filled over-enthusiasm toward Froome, the four-time Tour victor from Team Sky who was cleared of doping accusations days before the Tour began earlier this month.
"Months and months of waiting [for the anti-doping case to end] fuelled the suspicion and it took its toll", said race director Christian Prudhomme, who informed Team Sky that Froome was not welcome at the Tour before he was cleared of doping.
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He managed to get back on the bike and bridge the gap to the leaders, leaking just 13 seconds to the triumphant Geraint Thomas, but called it a day after learning the extent of his injuries. I want the fans to respect the riders. "They make the riders breathe in noxious air, and they blind them", he added.
Defending champion Chris Froome, who has often been subjected to negative treatment from Tour de France fans, was booed all the way up to the summit and one spectator ran alongside the Briton before slapping him on the shoulder. Primoz Roglic was fourth at 2:46, and Romain Bardet was fifth at 3:07 back.
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 to win by a wheel length.
Sagan's 11th career win at the world's biggest bike race came after he was the fastest to the line in bunch sprints on Stages 2 and 5.
Fernando Gaviria and Dylan Groenewegen, who both won two stages on this Tour, along with Andre Greipel all abandoned the race on Thursday, while 30-stage victor Mark Cavendish and Marcel Kittel failed to make the time cut on Wednesday.