This happens to me a lot as well. Clipping windfury and sword spec attacks is just something that happens occasionally, and you have to get used to it.
Its because although technically they are "instant" attacks, they still take place a short time after the initial swing happens. I find that if you constantly delay your slam just in case you were to get a wf/ss proc, you'd probably end up losing a similar amount of damage overall. Just a design flaw that we have to live with unfortunately.