The Dutchman was speaking after Wellington Phoenix were awarded the points as they led 2-1 when rain made the pitch unplayable and the match was called to a halt with 17 minutes remaining.
According to rule 22.22 in the A-League regulations, if a match is abandoned before the end of the first half, it must be replayed, but if it is called off during the second half, the score at the time is final.
The rule has been in place throughout the 10 years of the division's existence, but Thijssen found it perplexing when he discovered his team - who are chasing a play-off spot - would not have the chance to finish the game at a later date.
"Of course I'm disappointed because this is a crazy end," he said, having seen the result hand Wellington a four-point lead.
"If you always worked in Europe and you see this you think, 'what is happening here?'
"[I've] never seen this, because the choice is a replay if it happens in the first half, they're the normal rules, and if it happens in the second half you have to play the second half again.
"We all want an honest competition and Adelaide and Perth, they're not happy with this because they are in a competition to be the champions.
"And we're in a competition to be in the play-offs, so of course it's disappointing.
"When we had a free-kick in a dangerous position where we could score, they just call off the game and they give three points to one team and no points to the other team, that's not an honest competition."
