Overwatering is a possibility but I would expect that to affect all the seedlings rather than just 3 out of 5.
The yellow leaves does look like nutrient deficiency but, again, why would a couple of stems not be affected?
Seems more like something specific that's just affecting those 3 stems.
Are the affected trees on the sunny side or shady side of the clump?
Any chance of herbicide having been used nearby?
Need to have a closer look at those affected stems. Maybe scratch down to the surface roots to see if anything different on one side or the other.
How are/were the individual seedlings held together to fuse?
Just asking because if the ties are still in place that might be strangling those seedlings.