Cavendish was left fuming when his hopes of wearing the famous yellow jersey for the first time in his career were ended amid carnage in Bastia, where a team bus became lodged under the finish line gantry, in turn causing organisers to initially move the finish line by three kilometres before restoring the original route.
With those decisions made as the peloton was baring down on the town, the confusion was blamed for a major crash six kilometres from the line which ended the chances of not only Cavendish but also rivals Peter Sagan and Andre Greipel, with Marcel Kittel taking the stage win instead.
Cavendish used his Twitter account this morning to vent his continuing frustration.
"A bit upset after yesterday's [Saturday] finish, but have to count myself lucky compared to some guys who crashed hard. Feel so bad for @tonymartin85," he wrote, referring to team-mate Tony Martin.
The German world time trial champion bore the brunt of the biggest crash, suffering a concussion, contusion of the left lung, and a 5cm wide wound on his elbow which the Omega Pharma-QuickStep team said cut down to his muscles.
Amazingly, the team said this morning that Martin would take the start on Sunday.
But while Cavendish missed out on yellow, he was more concerned on Sunday with his main target for the Tour, the points leader's green jersey.
Although organisers awarded all riders the same time on Saturday due to the chaos, there was no such allowance made in the points standings.
With Kittel taking 45 for the stage win, Cavendish is already 36 points off the pace with nine for his efforts on Saturday.
"I'd love an explanation from @UCI_cycling as to why time was neutralised on yesterday's [Saturday] stage, but not points. Were only GC riders affected?" the Manxman wrote on Twitter.
Orica GreenEdge were fined 2,000 Swiss francs (£1,400) by organisers for the incident with the bus for "not respecting the timetable put in place for auxiliary team vehicles arriving at the stage finish".
The gantry is raised earlier in the day to allow larger vehicles to pass under, but had been lowered by the time the bus arrived.
However, the team have continued to insist their driver was only following instructions.
Sport director Matt White said on the team's website: "The bus was led under the finish gantry, and it we took for granted that there was enough clearance. We've had this bus since we started the team, and it's the same bus we took to the Tour last year.
"Our bus driver was told to move forward and became lodged under the finish gantry. He followed all instructions in the process that followed thanks to the hard work by ASO that allowed him to remove the bus before the finish. It was the best possible outcome given the situation."
After Saturday's relatively flat run alongside the eastern shore of Corsica, Friday's stage to Ajaccio is much tougher as the riders head into the mountainous centre of the island, tackling four categorised climbs.