Brighton chief executive Paul Barber says Moises Caicedo's decision to turn down Liverpool and join Chelsea left his club in a "difficult position".
Liverpool agreed a £111m deal for the Ecuador midfielder, 21, on Friday.
But on Monday he joined Chelsea for a £100m fee that could rise to a British club record of £115m.
Barber said Liverpool "couldn't have done any more" but Caicedo's "preferred destination" was Chelsea.
"Obviously in that situation we're in a slightly difficult position because we negotiated a deal, we spent many days working with Liverpool to get a deal agreed," he added.