The 27-year old striker has been heavily linked with a summer transfer to St James' Park recently but Aulas suggested that perhaps behind-the-scenes action has caused the deal has fallen over and indicated that he will be lodging a complaint.
"I am very disappointed that the deal was never finished with Newcastle," Aulas told L'Equipe 21 TV after Lyon's Champions League qualifying win over Grasshopper.
"Personally, I am very pessimistic. Someone is pulling the strings behind the scenes.
"I have filed a complaint for 'destabilisation'. Things will be settled in front of the appropriate committee.
"It is a complete disservice to Bafe. He is a player that we respect. It completely flipped over with Newcastle. It was a priority that Bafe should have got what he wanted in terms of salary.
"For the moment, the situation is blocked. On the 30th August, if no solution is reached we will reintegrate Bafe in the squad. We will have to change our approach to Bafe's situation. Our desire is to settle things positively for everyone involved."