No, I don't think you are doing anything wrong, it is just a coincidence.
Misting the trapped portion with plain water to soften the "skin"/membrane periodically can help the seedling to open, otherwise once softened you can try to remove it yourself, very carefully, with a toothpick or other pointy "tool". If you decide to remove it by hand, hold the stem in one hand gently before trying to remove the skin/membrane gently with your free hand. If you don't hold the stem gently when removing the skin/membrane, it is possible to decapitate the seedling, and yes, I am talking through experience.
Hope this helps,........
Organoman.