Krkic has joined Alaves on a season-long loan.
"Bojan is a difficult one," Hughes sighed. “From my point of view, I'd have preferred he saw his future here.
“I had an early conversation when he came back from the close season about where he felt his future lay.
“He spoke about his career and his personal life and I think that was the key element of the decision he made because he was very much in the mix against Everton (on the opening weekend).
“Players who don't play week-in, week-out aren't happy."
Asked if he could yet return to the fold, Hughes continued: “I hope so. If you look how his career has progressed since he left Barcelona, you would say his most successful period was here and we would like that to continue."