Maarten Tjallingii explained that he, "tried to get our riders into a good position but the wet track made it hard."
Team manager, Frans Maassen meanwhile was left confused.
"I just do not know what went wrong," he said before admitting that Freire and Matthews were too far back in the final group to make a difference.
"We had thoroughly discussed the rider's roles previously. Coen Vermeltfoort would be the last pacesetter in the train for our two sprinters. But the team was not there to set them [Freire and Matthews] up."
One possible reason for the team's confusion was the puncture that German Paul Martens suffered in the final kilometres.
"Too bad it did not go well," Maassen mused. "We have two men that could go, but on Tuesday there are fresh opportunities."
Stage 3 of the Amgen Tour of California is a 196.2km course from Auburn to Modesto that once again, should suit the sprinters.