Havertz has said that this season is not what he "expected it to be" and has been "stop and start".
The 26-year-old also said earlier this campaign that it was a new experience going through a major injury and he "hasn't really faced a challenge like this before".
He looked disappointed by the latest setback when he was taken off after just 34 minutes of Saturday's 1-0 win against Newcastle United.
The Gunners have been criticised for their attacking play this season and their reliance on set-piece goals.
Havertz is one of Arteta's favourite players on and off the pitch and they have missed his ability to link play.
Since his return he has played as both a midfielder and a forward, and Arteta has missed having that versatility when Arsenal are trying to break sides down.
Havertz has three goals and one assist in five Champions League games this season and scored the winner in Arsenal's Champions League quarter-final first leg against Sporting.
He has only started one game in Europe though, against Kairat Almaty in January, but came off at half-time as he built up match fitness.
Despite his availability issues, Havertz has five goals and four assists in 20 appearances, giving him a goal involvement of nearly one every two games which highlights how Arsenal miss him when unavailable.
But they have not been able to call on him nearly enough and Havertz has been restricted to just six starts in the Premier League.
As the season has progressed, there have been doubts about whether Gyokeres is the right fit for Arsenal, particularly against elite opposition.
When Havertz was fit, he started and scored against Manchester City, with Gyokeres on the bench in what was a glimpse at what would likely have been Arteta's strategy for big games if the German was fit more often.
Havertz scored by pressing City goalkeeper Gianluigi Donnarumma, and without his work-rate and intelligence for large parts of this season, the Arsenal attack has looked clunky at times.
