I actually had something like that happen once! I just use peat-pucks and place seeds about 1/2" down and make sure they are nicely covered, I don't pre-soak or anything. I couldn't figure out what was going on when I had a nice normal looking sprout with a strange tentacle sprouting from the base, it was kind-of a race between the tentacle and the baby for a while before I figured out that it was the tap root and replanted it :-)