Scotland coach George Burley admitted they were second best to the Dutch but was angry at referee Laurent Duhamel.
Gary Caldwell had a headed effort disallowed and Burley spotted foul play at the second goal for the Dutch.
"There were one or two decisions that went against us," Burley told BBC Radio Scotland after the 3-0 defeat.
"Allan McGregor was blocked for the corner and then we scored a perfectly good goal and no one can work out what the referee's given a free kick for."
Caldwell found the net with a powerful header midway through the second half but Duhamel signalled that there had been a prior infringement in the penalty box.
It was a rare foray forward for the Scots, who spent most of the match pinned back in their own half and conceded two very soft goals in the first half.
However, Burley was frustrated to see a possible lifeline cruelly snatched away.
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"It was a poor decision," he added. "If we get the goal that would have spurred us on at 2-1 and you don't know what's going to happen."
Klaas-Jan Huntelaar and Robin van Persie both found far too much room to score with first half headers, although Burley questioned the legality of the second goal, with goalkeeper McGregor impeded by an opponent.
"We worked hard before they scored and we maybe conceded a free header for the first goal," Burley continued
"Going in at 1-0 you still think you can get something from the game but then we conceded again right on half time.
"We had one or two chances before they scored and you don't get many against Holland."
Lone striker Kenny Miller had been given a clear sight of goal on 15 minutes but delayed shooting and was caught by a Dutch defender on the edge of the six yard box.
Shortly after Caldwell's disallowed effort, Dirk Kuyt added a third goal for the home side from the penalty spot, following Huntelaar's topple under a challenge from Wolves defender Christophe Berra.
And Burley was full of praise for the team who lead Group 9 with four wins from four games.
"All credit to Holland," he said. "They are a tremendous passing team, with great movement. Going forward there are not many better teams in the world."
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