Mercedes team principal Toto Wolff conceded to being caught out by Red Bull's mid-race "gamble" to put Dutch Grand Prix winner Max Verstappen on the hard tyre.
After switching Hamilton to the medium compound at his second stop at Zandvoort, Red Bull responded immediately, although placed Verstappen on the hard Pirellis.
With very little running completed on that tyre, the decision was one Mercedes had not foreseen.
"I think the hard tyre was a bit of a gamble," Wolff told Sky Sports F1. "You could see on the Ferraris it was going well but it was unknown territory.
"None of us had really run it. We didn't run it at least."
In boxing early, Hamilton returned to the track amongst backmarker traffic and was unable to gain time on Verstappen.
"I think we had a sniff of an undercut there," explained Wolff. "We didn't time it right. In the end, you are always more clever.
"We didn't expect them to go onto the hard tyre because it was an unknown. We didn't drive the hard tyre on Friday and we thought we might be pushing them early with the soft but it is what it is.
"When you have the quickest car on track, whatever you try on strategies it is difficult but credit to him, credit to Red Bull, they were faultless today."