It isn't unusual for this to happen. What you may be seeing is the seed case. I keep a small container of vermiculite handy and when this happens, I pour enough over them to cover the seed case, so that it is covered. You can do the same with the potting soil that you are using. I only plant my seeds the depth of a pencil eraser. It may be that your potting soil is too dense and isn't allowing the radicle (or tap root, as I call it) to extend down easily through the soil, so the new growth is pushing the seedling up instead of down.

Nancy