At the time, it seemed to be a reasonable suspicion.
ISIS has been openly bragging about how many of their members they had infiltrated into the flow. A passport was initially found that linked one terrorist to the refugees.
Given the uncontrolled entries into Europe, it's highly likely some of them are ringers. The major flow into Europe just started last summer, so it's way too soon to make the call that this isn't going to be a problem.