It had appeared that the Ghanaian midfielder suggested race played a part in the Arsenal selection policy.
Having been asked on the social media site why he wouldn't be playing, Frimpong had replied "LOL I wanna laugh", before following that with "Sometimes I wish I was white and English #realtalk"
Quickly realising the conclusions drawn by many, he soon assured fans "Not every tweet is football related", though the headlines had already been made.
Arsenal succumbed to a 2-0 defeat to rivals Chelsea last night and could have used Frimpong's battling qualities in the centre of the park.
The former Fulham-loanee failed to even make the bench, with Wenger claiming the 21-year-old was short of fitness.
Wenger has since spoke to his young player, and was assured that the comment was merely meant as a joke.
Speaking to Arsenal.com, Wenger said:
"No, he said it was a joke. I don’t know [that] has he a problem with England, with anybody else, with Arsenal."
And the Frenchman - who watched on last night as Arsenal played poorly against the Blues - also revealed that Frimpong was in fact called up as a back-up but fell sick.
"He was on the list to be the 19th player, he was called up this morning but he was sick. So for us, he was selected."
Wenger now guiding his side through a horrendous run of fixtures, follows up defeat to Chelsea with a home tie against Liverpool.
The Gunners will be glad to return to league duty, as their last two defeats came in cup competitions.
The home side will likely recall Mesut Ozil, and the German along with his team-mates will be looking to cement the North London club's place at the top of the table.