Essendon believed it had a deal with ASADA in which the anti-doping agency would not impose any penalties on Bomber players, according to chairman Paul Little.
A string of emails leaked in the past week appeared to indicate a deal between ASADA and the AFL dating back to the preliminary stages of the 16-month investigation into Essendon's controversial 2012 supplements program.
Little indicated on Channel Seven that such a representation had been made to the club.
"Certainly we were of the view that there had been an accommodation reached, an agreement reached. We were very surprised when we learned that ASADA had decided to go back on what was the original agreement," Little said.
Despite believing they would not be subject to any sanctions, 34 players who were on Essendon's 2012 list were handed show-cause notices by ASADA on June 12. An extension was granted on Thursday and they now have until July 11 to respond to the allegations that they injected banned substance Thymosin beta 4.
Little flagged that the round-the-clock speculation and media coverage was affecting players.
"Some of the players are handling this better than others. There's no question that when you wake up every day and it's in the papers, on the radio, you just can't escape it. Your friends are asking you about it. It must be front of mind for them. I know the players have been very brave and they've been asked to handle this for quite some time. I think at the end of the day it must take its toll."
Little said the Bombers had been left with "no choice" but to challenge the legality of the ASADA-AFL investigation. The directions hearing in the matter will be heard in the Federal Court on June 27. Suspended Essendon coach James Hird simultaneously will be challenging the joint investigation.