Despite finishing 10th in the final bunch sprint where Mark Cavendish (Dimension Data) triumphed, Groenewegen had done enough to keep the race lead.
But after suffering a mechanical in the final 70 kilometres of the stage as echelons formed up the road, the race officials didn't like his slipstreaming behind the LottoNL-Jumbo car and slapped him with a 20 second penalty.
“Right at the moment when echelons were forming we had to give Dylan a new bike," sports director Jan Boven said. "Moreover, that didn’t go completely smoothly. That’s our mistake and we are being punished for that by a time penalty."
While Groenewegen accepted the time penalty, he expressed frustration with his team's mechanics which Cyclingnews captured.
"It was my goal to win the Dubai Tour but now it's really difficult. Maybe we'll see on the last day. It's the fault of my mechanics.
"My second bike was f*ked too, that's why I changed it. It was the bottom bracket. It was completely f*ked!"
The Dutchman now sits 42nd overall.