You might just have a derp seed is all. Your first true node looks like it's throwing clubbed leaves. I can see by the soil shading that we need to talk about watering. There's a wet region and the stem is sitting in the middle of it. What it should look like is a wet ring around the plant away from the stem. When you water, try doing it with a spray bottle set to "stream", and spray in a circle around the seedling about 2 inches away from the stem all the way around. As the plant grows you will expand that watering ring to fall on the dirt roughly where the leaf tips extend to. This is what is called a plant's drip line.
The warble on first node is different than the clubbed leaves at the second. That warble is usually uneven cell growth very common in seedlings while they are figuring out their calcium regulation and they outgrow it. Don't worry too much about the cotyledons yellowing. That is supposed to happen, but not too quickly. The cotyledons carry all the nutrients the plant is eating until they can pull them up from their young roots. Overwatering and overfeeding will make them yellow prematurely.
A little seedling in a big pot isn't the problem some people think it is. You care for it as if it's growing in the ground, so you're watering the drip line and not the whole pot. Until the roots properly occupy the medium, that's how you should water.
