This is so odd, I seem to have the same problem with a couple of my pepper seedlings... one has cotyledons and no true leaf, another has one set of true leaves and.. no growing shoot...
The leaves look fine though, so I'm going to wait a bit more and see what happens.
Also had three tri-cotyledon pepper plants this year - from different seed sources, no clue how this is caused... They were slower to leaf out but appear to be developing more or less normally.
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