This is my first attempt. So I'm a noob. I just thought the stem grows up with the seed casing and not the other way around. So the routes will sprout out of the seed that is in the hole? So how do you tell the difference between the root and the stem?
This is correct. The root will be the first thing you see come out of the seed, then the stem and finally the cotyledons (baby leaves) will unfold. A lot of times the seed hull will stick and the little leaves can't pop out. That's what I was saying about the tweezers. I don't use alcohol to sterilize my tweezers, I just use em, but it's probably not a bad practice to do so.
Now, am I to understand these are still in the dark? I ask because (this is only a theory, someone will probably dispute it) if there is no light, and the seed wasn't set firmly in the rockwool cube to begin with, I don't believe it impossible for the root to come out the top. If you're certain, and only you can make the call at this point, that is the case...flip it around. Be very gentle with the root, it's incredibly fragile.
If I'm analyzing the photo correctly, the plant on the left is an upside down U shape (n?) and both the end of the taproot, as well as the seed pod, are "under ground" and the stem is up? right? If this were mine I would (did I say gently already?) "help" the seed side up a little. Again, people here will say this is a process that has happened a trillion times in nature and it will figure it out, and they will be right. However, my seedlings never do what the fuck they're supposed to do!! 80% of the time mine do something like what you're seeing, or don't shed the hull like I described earlier. Or shed the hull and keep the fucking membrane holding the leaves together. The "solution" to this is planting deeper, something about the friction of the plant growing through the medium stripping the hull from the tiny plant on its way up. Doesn't work for me. Just help them if they look like they need help, and if you fuck them up...try again. Experience is the best teacher and eventually you will have seen every...eventuality...that can arise.
In the mean time, put a light over those things. I use a fluorescent desk lamp with a generic "plant" bulb in it. They are only going to be under it for the next 3-4 days so I don't do anything fancy.
Finally, use your flash. It's ok. Take better pictures. Keep asking questions. We will help. Happy growing, and best of luck!