Rev hit it, but on zig zag, usually your tensions are a lot lower and you can end up with the knot on one side or the other, usually the bottom. A zig zag stitch is used to allow a little stretch in the seam. That's why it doesn't matter if the knot is on the bottom, functionally.
If I were making a sail and my stitches looked like your picture, I would try to adjust a little but not fret if that is how they turned out. 2 reasons, it takes A LOT of tension to pull a knot into the middle of dacron without using a needle too large AND it's still a functional stitch that is designed to stretch a little.