Click tracking is very reliable, so I bet that isn't the exact issue. That said, has the percentage or absolute number changed? I've seen many cases where when someone switches to Marketo they bring over a bunch of junk leads which had been flagged as undeliverable in the old system, but which aren't that way in Marketo.
If you haven't, it might be good to talk to support- we offer best practice advice on email deliverability.