I know going into the West Ham game we had conceded more counter attacks than anyone else in the league and in games since (like the Villarreal game) it seemed like an inability to function in defensive transition was our achilles heel there too.
Basically we struggle to control the game well enough to either supply a constant stream of good chances or nullify threats on the counter. And by "control" I don't mean possession so much as structure. Once we surrender possession it's too easy to cut through us.
That said, clean sheets aren't measure I'd use to judge.