The midfielder returns to the Emirates Stadium with Chelsea this weekend, knowing victory will put his new side on the verge of the Premier League title.
After being sold to Barcelona in June 2011, Arsenal were understood to have first option should the 27-year-old come back onto the market.
A potential deal, though, never materialised as Fabregas ended up joining Jose Mourinho at Stamford Bridge.
“I cannot speak to you about that (reasons) now because that will not help us to win the game on Sunday,” Wenger said.
“We will have to discuss that one day, with all the terms. It is not as clean as that.
“The regret I have is that he wanted to leave here. This club and myself had a very positive influence on Cesc’s life, so I would be a bit uncomfortable to have to justify today why he is not here. I believe I would rather it was the other way around.”
Arsenal were thumped 6-0 at Stamford Bridge on Wenger’s 1,000th match in charge last season, and matters off-the-field took centre stage.
Wenger was keen to play down suggestions of a dispute between him and Mourinho which flared up that day, and wanted to take attention away from the men in the dugout.
“It is not a confrontation (between managers), it is a confrontation of two teams. Football is down to the fact that the performance on the day will decide the game and the result, so let’s focus on that,” Wenger added.
“We have not always lost, first of all, in 12 attempts. We have come close to beating them a few times and they have always had very strong teams.
“We are on a good run and we have an opportunity to beat them at home, and we want to take it.”