Sprinter Caleb Ewan got tangled up in a crash on a descent with Jurgen Van den Broeck (LottoNl-Jumbo), and injured his shoulder. He tried to continue, but dropped out after riding for a few kilometres.
His exit followed that of teammate Roger Kluge, who, according to the team, has been suffering from a fever and illness over the past few days.
"Of course it is very unfortunate," said sport director Matt White. "With Roger we knew that he was struggling yesterday, but the crash of Caleb was totally unexpected and is really a blow. The one positive is that he doesn't appear to have broken anything and will hopefully make a speedy recovery."
Yates, fresh off a victory in the GP Industria & Artigianato, finished seventh on the stage and is 24 seconds off the lead of BMC's Greg Van Avermaet.
"Clearly the focus has shifted more onto Adam now," White said. "There was no need for him to push on today or take any risks and he rode very well at the end to keep himself up there with the other overall contenders."
With two more days in store for sprinters, the team will have to change up its strategy, perhaps freeing up Luka Mezgec or Daryl Impey to contest the sprints.
"For sure it changes the complexion of the next couple of days for us," White said. "Caleb was second last year on what is the finish of tomorrow's stage and it was a stage we had been targeting. Nevertheless that's cycling, anything can happen at anytime and we will adapt and move forward."