The Ford squad had started the WRC’s visit to Africa on the front foot, with three cars inside the top five after Friday’s opening stage.
However, as the day progressed M-Sport’s fortunes worsened, beginning with nine-time world champion Sebastien Loeb retiring from fifth after Stage 4.
Loeb had won the day’s first stage, but his engine cut out after finishing the last test of the morning loop. A small fire in the engine bay reduced the Frenchman to electric power for the the road section, but a depleted battery ended his day five kilometres short of the service park.
Team-mate Gus Greensmith lost 13 minutes to a right-rear puncture that damaged his wheel rim and required a wheel change on Stage 4, while Adrien Fourmaux retired on Stage 5 with a rear differential problem.
To compound matters further, Craig Breen was forced to stop to fix a puncture on the day’s last stage before a steering failure sent him off the road. The Irishman's day was ended prematurely in the incident, which took him out of sixth position.
The way the day imploded left Wilson dumbfounded, while revealing the failure of a component that cost 10p had resulted in Loeb’s retirement.
“I can’t remember when we lost all three points-scoring cars on the first day, honestly I cannot remember the last time that happened," said Wilson.
“Unfortunately the piece that failed [on Loeb's car] probably cost about 10p. It was a small O-ring that failed, which caused a leak and then the thing caught fire and burned the dome of the wiring.
“It is an amazing rally and the character of it is unlike anything else in the world.
“Personally, I think the fesh-fesh sand is spoiling it to be honest, if you see what has happened to a lot of the cars. But if all the rallies were the same, we wouldn’t get this kind of adventure.”
Team principal Richard Millener added: "I still think the car is really strong, but we have just had freak accidents and freak issues with every car.
“There is nothing we can do but pick ourselves up."
M-Sport has struggled for consistency since three of its cars finished in the top five - and Loeb claimed victory - at January’s season opener in Monte Carlo. Breen’s second place last time out in Sardinia is the Cumbrian outfit's only other rostrum finish so far.
Breen was also surprised by the way his Friday ended, having driven carefully through Kenya’s tough gravel and sandy stages.
“It has been a bit of a disaster to be honest, all of the team has had a tough day,” Breen told Autosport.
“I was happy with everything that was going on, happy with the speed and happy with not making any mistakes.
“I wasn’t putting the car in any danger and what happened on the last stage was a bit of a disaster to be honest.”
Looking ahead to Saturday, M-Sport plans to repair its entries for Loeb, Breen and Fourmaux, who are all scoring points this weekend and is hoping Kenya’s attritional stages will help in salvaging some points.
“Last year Kalle [Rovanpera] retired on the last stage of day 1 and I think he ended up finishing sixth, so the target is to get all the cars back out," said Wilson.
“After today, anything can happen.”