Which is the precise argument that the other side is making. When we special-case terrorism we're no longer on solid ground - whether it's in favor of looser or stricter treatment.
So, here's the thing: the level of false positives, when calculated in aggregate can suggest unreasonable enforcement. If 95% of all searches yield nothing, there is a legitimate question of whether or not your targeting is reasonable. This is the primary legal argument being used, for example, in the ACLU's case against NYC's stop and frisk policy.
But a single case of a false positive, with no further information, cannot be taken as evidence either way. The fact that the Wall Street plot may have been a false positive sheds no light on whether or not the suspicion was reasonable in the first place.
I think you're making a category with respect to traffic stops, though. It's not "law enforcement" at the point the searches are being done in the context of surveillance, and I'd argue that meatspace comparisons here are inapt on the whole. The level of inquiry through surveillance would be comparable to a LEO having reasonable suspicion of something, then downloading your GPS history and searching your car after you leave it at your destination (imperfect, but close enough for internet debate).
In this case, it should be! Keep in mind the kind of evidence they were working with.
And nobody's talking about traffic stops, but call me crazy when I say I think terrorism should entail a slightly higher standard than that.