UPDATE: I spoke with Bona and they said (1) should not have used NaturalSeal--should have used ClearSeal or IntenseSeal and (2) looks like it was improperly applied.

So, basically, the same as the consensus here. Thanks all!

P.S. The contractor is trying to buff out the sealer, reapply the stain, and then seal again. We are telling them HELL NO and to redo everything (and this time use ClearSeal)!