The France youth international was reported to have been involved in a bust-up with Arteta at the club's warm weather training camp in Dubai during the mid-season break.
Speaking at a news conference ahead of his side's Europa League clash with Olympiacos on Thursday, Arteta revealed the 20-year-old's absence was related to issues with how he was training.
"I just do my team selection in regards to how they train, how they play, how they behave and every week it will be different," he said.
"One week it will be one reason, one week it will be another reason. It was about the way we trained, the way we live and I want the best players for the game and I select them in relation to what I see on a daily basis."
Guendouzi has been named in Arteta's squad for the last-32 first-leg clash in Athens, but the Spaniard refused to confirm if he will be selected in the starting XI.
He said: "We had a break of 15 days. We played just one game so I'm going to send out a team that I think is the best to play.
"The rest of the game will take care of itself. We cannot control everything. Sometimes you think about resting somebody and in training he gets a little issue or he gets sick.
"So, we will send out a team that we think is the best to beat Olympiacos and the rest of the teams after that will take care of themselves."
Arteta has also not ruled out that Pablo Mari could feature for the Gunners for the first time against Olympiacos.
Mari is yet to appear for the first team since joining on loan from Brazilian side Flamengo in January, but Arteta has suggested that he could be involved soon after coming through a reserve team game earlier this week unscathed.
Arteta, who was not present at the match, said: "I could not be there for a personal reason. I was pleased they [his staff] were there.
"His [Mari] commitment has been really good. He did well the other day and hopefully soon we can start to use him."