Emily, are all the affected seedlings in one batch? I never had that issue but mine stayed in until they were more mature.

Looks like it might be insect damage--I doubt it's a nutritional deficiency--and you could spray with some insecticidal soap in the evening after the sun goes down, then watch carefully to see if newer leaves grow in normally.

Don't despair, though; strong seedlings will shrug off some insect damage and grow just fine.

Thanks Jen, I'll get some insecticidal soap on the way home today. They are all from the same batch, but I suspect bugs just because there are so many everywhere and how they cause leaf deformations and things like that. They started out without those deformations and have produced 1-2 sets of leaves without any problems, and then now almost all of them are developing this same issue. Thanks for the encouraging words, I'll treat them tonight and keep watch on new leaves.