Agüero didn't join up with the national squad this month because of this, missing out on a 2-2 draw against Germany and a 6-1 win over Ecuador.
The Premier League's joint-top goalscorer this season has been in fine form with his club side, but there are now growing fears that he may be yet another name added to Pep Guardiola's injury list.
Reported by The Mirror, Scaloni stated: "Sergio Agüero is not here [with the national team] because he's been carrying a problem and has not been training 100% with his club".
Lionel Messi was also absent from the Argentina squad as well, and there were concerns that these injuries would cause them problems, but Scaloni's side end the international break unbeaten, and expects both forwards to be fit again in time for November's fixtures.
Sergio Agüero is expected to return to Manchester City training at some point this week, but Guardiola will be no doubt worried about the fitness of his star forward.
City are already without Aymeric Laporte and Leroy Sané until 2020, while Kevin De Bruyne and John Stones have been carrying knocks. With a huge uphill battle to try and retain the Premier League title again, they could do without Agüero being added to this list in the long term.
They face a surprisingly in-form Crystal Palace side this coming weekend, the only team to beat City at the Etihad Stadium in the league last season, and City will be hoping that talisman Agüero is fit to play a part.