Sure there is. The equation only cares about one specific point in time.
0 m/s2. That doesn't matter, because you're misapplying F = ma. The equation's used to tell what force could have caused a given acceleration, or what acceleration is created by a specific force (or a few other permutations on that).
You need to remember that with gravity as you're standing on a scale, you're experiencing not one but two forces. They're equal and opposite, so yes, there is zero net force being applied. The forces cancel out. But that does not mean that there is no force being exerted on you at all.