The doubles pair lost Monday's third-round match 6-3 4-6 6-4 3-6 14-12 to Jonny Marray and Adil Shamasdin.
The first code violation came after umpire Aurelie Tourte refused Cuevas a toilet break; the Uruguayan then showed his frustration at double-faulting.
"You have to take bad calls on the chin at some point," said Britain's Marray.
The earlier code violation was handed to Cuevas for unsportsmanlike behaviour when he threatened to wee into a ball can after being told he could not leave the court to visit the bathroom.
He then angrily smashed a ball out of the court following a double fault and the 15th seeds were docked a point, resulting in Cuevas and his partner sitting down and refusing to play the final game.
A supervisor had to be called.
"I went to the bathroom twice during the match and obviously the fifth set was a long one. I think you should be allowed an extra toilet break if it's five sets," said Marray.
"You have to respect the officials regardless of whatever happened in the match. You can have a word or two but they're trying to do a job and you have to respect that."
Shamasdin added: "I don't think the chair umpire really had the match controlled. She made a few mistakes early on at both ends. We were all on her and she was definitely flustered. I don't think she handled it correctly."
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Farrell, 25, is set to move past 500 international points this weekend against Fiji, and is second in the England all-time list behind Wilkinson.
Asked whether Farrell could one day beat his record of 1,179 points, Wilkinson said: "I have no doubt.
"I would be very surprised if Owen Farrell didn't go on to score way, way more," he told BBC Sport.
"500 points for a guy who is 25 years old, you don't have to do the maths but if he plays until he is 35, he will be in a good place."
Wilkinson has been involved in the England camp this year as a kicking and skills consultant, and says he can identify with the way Saracens fly-half Farrell approaches the game.
"Sometimes when we are discussing things, you hear something that you definitely correspond with," said Wilkinson, who on Thursday became one of 12 new inductees into the World Rugby Hall of Fame.
"[Working with England] is a really exciting opportunity," Wilkinson, who scored the winning drop goal in the 2003 World Cup final, continued.
"But there is no telling or teaching, it's kind of a sharing, and therefore there has to be room in all of us to keep growing. I am also there to learn."
Wilkinson has also compared the current midfield combination of Farrell, who has scored 497 points for England, and fly-half George Ford to his partnership with inside centres Will Greenwood or Mike Catt.
"Both those guys were phenomenally important to me in my career, in the way they supported me, got the best out of me, and helped me to uncover more about myself," Wilkinson explained.
"With Owen and George, they are both very, very open individuals, both very humble - but not because they have been taught what to say, but genuinely it's who they are.
"There is not a script being followed here. They are following enthusiasm, passion and serious devotion.
"It's very similar when you mention names like Mike Catt and Will Greenwood, it all makes perfect sense. It's just about having good people in there."
You can hear more from Jonny Wilkinson on the Matt Dawson Rugby Show on BBC Radio 5 live from 19:30 GMT on Thursday, 17 November.
Pablo Cuevas and Marcel Granollers held a sit-down protest after receiving warnings for threatening to wee in a can and hitting a ball out of court.
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World Cup winner Jonny Wilkinson has backed Owen Farrell to overtake his England points record.