The Serie A champions slumped to a 1-0 UEFA Champions League defeat in Greece, their second consecutive loss in Group A.
That defeat followed the end of Juve's 100 per cent winning league record this season as they were held 1-1 at strugglers Sassuolo last Saturday.
Juve's results in the past week have seen the side come in for criticism, but Allegri believes the team's performance in Athens did not warrant such negativity.
"On Wednesday we had three players in the starting XI who started training with the team 40 days late," he said ahead of Sunday's clash with Palermo at the Juventus Stadium.
"We are trying to improve certain things, but I was without many players for 15 days due to international duty, which is positive in that it proves I have talented men at my disposal.
"I think the team was unjustly criticised. We conceded one goal in Athens on a ball we lost in midfield and attacked them a great deal. We have every chance of qualifying and can mathematically still top the group.
"We will analyse the defeat, because we did not play well and didn't control the game properly. However, the first 45 minutes in Athens cannot justify such ferocious criticism.
"In Serie A we've won six games and drawn one. It's nice trying to win all the time, but considering the circumstances few expected us to be top of the table already with Roma such tough opponents."
There was some positive news for Allegri this week after much coveted midfielder Paul Pogba ended speculation regarding his future by penning a contract extension until 2019 on Friday.
The France international has courted reported interest from the likes of Chelsea and Manchester United and Allegri is delighted the 21-year-old opted to remain in Turin.
"I think the club invested well in this 21-year-old player," he added.
"He has to improve a lot, as he is lacking that last step to become extraordinary. He has a great future and can stay here for a long time."