The France international looked set to join the Toffees on the final day of the summer window, but changed his mind at the last moment and ended up joining Spurs from Newcastle United in a £30million move.
Koeman said: "Overall (the window was) positive, because we signed some good players.
"Of course, we had a disappointment on the last day, but that happens in football, because you don't get always what you like to have.
"It was not in our hands with Sissoko. He chose finally a different option, but I can't say anything against the club, the board, the chairman, because we did everything to get the player.
"I did not have the meeting with his agents. From the outside, it was difficult.
"I spoke to the player, I think it was 10 days before the last day of the window - and the player showed his interest in coming to Everton. Then, finally, everyone knows what happened."