You are correct that the seed should not be half way down the container. It should be 1/2 inch or so below the top. Maybe when you watered it the soil settled. You should soak your container, then insert the seed and keep warm and moist.

For the other one this is normal. It's probably kinda shocked at the light and the new environment. You do have the light back aways, don't you? As long as it looks like it's not moldy or dieing it will probably grow soon. Remember warm and moist. (Sorry I aint stinky.)