It's hard to tell exactly but in the first pic it looks as though the sprout is still attached to the embryo/cotyledon, which has turned brown and seems to have a bit of fuzzy mold at one end. The brown thing shaped a bit like a bottle is the embryo/cotyledon. I'm not sure why the shoot was brown at the base, so there could already have been something wrong, but there definitely is something wrong now that poking around has detached the shoot completely. There should have been a root first before the shoot grew. My guess is that the seed became infected with fungus and rotted. Is there any sign that there was ever a root?
This is a daylily embryo taken out of its seed, yours looks the same only brown:
This is what a germinated seed should look like (I took off the normal black coating to make it germinate faster so pretend it's still there
The long white part on the right is the root, the light green part emerging on the top is the shoot:
