I'd like to think Trivkovic did this on purpose, a brilliant idea to cause a bit of chaos, for he too must have been bored beyond caring what was happening. Until then the Belgians had been playing like second class amateurs and Ajax had already scored and took their time passing the ball back to the goalkeeper for minutes on end. I'd like to think so, but probably the Croatian - UEFA Cup veteran - referee was just a little bit confused. And his confusion and lack of leadership at that moment caused a chaotic situation and a lot of anger among the players and the spectators.
The resentment was also caused by the fact that almost everybody agreed that Ajax' fist goal was scored from an off-side situation. Rewinding the match many times, I'm still nort sure. But bad or seemingly bad decisions by a referee can accumulate into something hostile.
Zulte Waregem is a bit of an exception in modern football. Not all players are full-time professionals, even the coach has a real job. Their stadium wasn't up to UEFA standards and still they managed beat Praha (3-1) and Austria (4-1). Zulte Waregem played with only two non-Belgians.