The 27-year-old defender ruled himself out of Celtic's second qualifying leg against AEK Athens - which the Scottish side ended up losing 2-1 - although boss Brendan Rodgers had said Boyata was fit for the game.
Davies remarked: "Dedryck has had a long chat with the manager.
"It is an unfortunate situation. We can't change what happened. There was a frustration, obviously, and the manager is managing the situation."
The 'Bhoys' rejected an £8m bid from Fulham for Boyata before the deadline, though Boyata could still move elsewhere in Europe with the transfer window open in Spain, France and Germany until August 31st.
Davies added: "There is no point vilifying anybody or blaming one individual.
"Obviously there has been a lot of frustration from the supporters but, as it stands, he is still a Celtic player and that may well be the case when the window shuts, so we can't say he will be leaving the club."