Froome, in his bid to become the first rider since deceased Italian great Marco Pantani, in 1998, to complete the Giro d'Italia-Tour de France double in the same year, won the Italian 3-week race in June.
"I would like to offer my honest apologies to both Elie Gesbert and Team Fortuneo for this unacceptable incident".
Sky, though, started the race under a cloud.
Team Sky also tweeted a video statement from Moscon, apologising for the incident.
Team Sky initially worked to keep the group at five minutes, but soon let them off the leash as Sagan claimed maximum points at the intermediate sprint and Alaphilippe led the way across the first climb.More news: Donald Trump backtracks on Helsinki remarks, says he 'misspoke'
"Like I've said, who knows what's around the corner, so (it is) each day as it comes", Thomas told a news conference on Sunday after a smooth ride in the 15th stage between Millau and Carcassonne.
For a third straight day, Thomas heard some boos as he appeared on the podium to collect his yellow jersey in Valence.
Omar Fraile (Astana) won the stage by being the best up the final climb. That pause precedes the four days in the Pyrenees, followed by the individual time trial on the penultimate day of the race. We just made sure we were there in the front.
But the 32-year-old's dream of upstaging the four-time champion Froome to become the Tour's first Welsh victor is being challenged on all fronts. Primoz Roglic gained time on the trio, but their other GC rivals were dropped on the final climb.
While the atmosphere within Team Sky seems to be peaceful between the two leaders - unlike in 2012 when Froome and eventual victor Bradley Wiggins were at odds - the British outfit has had to face boos and jeers from the French fans.
The flare was the only thing that came close to upsetting a relatively quiet day for Thomas after the drama of his back-to-back mountain stage wins which thrust him into yellow.
"It was very lovely to win today after three days in the Alps", said Sagan, whose 11th stage win on the race helped take his tally in the points competition to 398 points. "What happened was wrong and was a bad example coming from me to everyone", he said. The second summit finish tightened Thomas's grip and raised genuine questions about whether he would be allowed to try to win the Tour de France. "I played my card, went all in and lost", said a rueful Stuyven on the finish line. A group of 32 riders took off, gaining an advantage of nearly 10 minutes on the peloton.