MS Dhoni revealed there had been "unrest" in India's dressing room prior to Australia claiming victory on day four of the second Test.
The match in Brisbane appeared delicately poised when India began day four on 71-1 in their second innings, trailing by just 26 runs.
However, Dhawan - unbeaten on 26 overnight - was initially unable to continue his innings after taking a blow to the hand when batting in the nets before play, and India subsequently collapsed to 87-5 and 117-6 before the left-hander returned to the crease.
Australia went on to dismiss their opponents for 224, despite Dhawan reaching 81, and knocked off their target of 128 for the loss of six wickets to open up a 2-0 series lead.
Speaking after the match, Dhoni conceded there had been frustration after Virat Kohli was pressed into action at short notice on the fourth morning.
"There was miscommunication in our dressing room about whether Shikhar will go in to bat or Virat will go in to bat," India's captain is quoted as saying by ESPNCricinfo.
"I don't think we really handled the situation very well. I think the only way out of that was for the batsmen to spend a little time [preparing]. But we were not able to do that.
"We were having a bat in the nets and you know the wickets were not very good and he [Dhawan] got hit. But he didn't really react too badly there so we thought it's one of those where you get a hit but you are fine to bat.
"But by the time we came back he was really feeling the pain and he was not really in a position to go in to bat.
"I felt we were able to give only five to seven minutes' notice to Virat that he's going in next and I believe to some extent it created a bit of unrest in the dressing room and from that we were not able to get back. I would say that was one of the shortfalls, one area where we should have handled better."
A statement from India's team management criticised the condition of the practice wickets at The Gabba.
It read; "Team India has been asking for fresh net practice wickets at The Gabba several times for last two days but our request has not been met. We have been asked to practice on worn out wickets with uneven bounce, because of which two of our batsmen have injured themselves today [Saturday].
"One of the two batsmen, Shikhar Dhawan " who was one of the overnight batsmen on the fourth morning of the Test " had a right wrist injury due to which he was unable to bat in the morning. He is been examined by our physio, who will assess his fitness in time."