The Latics were looking good for a draw at the DW Stadium but conceded a late goal to Junior Malanda which hurt their hopes of progressing to the knockout phase of the competition.
Wigan will now need to beat NK Maribor in Slovenia on December 12 and hope Rubin Kazan avoid defeat to Zulte in order to make the Round of 32 which prompted Boyce to suggest losing in the manner they did was a major disappointment.
"Very disappointed. I thought we were controlling the game especially in the first half," Boyce told BT Sport.
"The first (Zulte-Waregem) goal was a bit soft from our point of view and we couldn't quite get a foothold back in the game.
"The second goal was a hammer blow for us. We thought we'd done enough to get a result here.
"Now we have to go to our last game and get a victory, and hopefully the other team does us a favour."
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