It's a genetic variation that is seen with various self-pollinating plants with dicotyledonous seeds. It isn't a bad thing as the cotyledon simply provides nutrients until the plant can begin to photosynthesize on its own. I don't think there is very much written about it concerning peppers. Follow the link below for details regarding sunflowers, which may or may not provide further insight. :)

Here is a link that might be useful: Preliminary observation on a spontaneous tricotyledonous mutant in sunflower

I've seen this in seedlings before but never found it too be an issue. I'm assuming it has something to do with the auxin which is in charge of cell division at the growing points.

Vera

I've seen it alot among my seedlings as well. I even sprouted a 4 coytledon Habanero White Bullet this year, that sure is a weird looker

I have had this happen to one of my new mexicos this year looked weird but hasn't caused any harm to the plant so far

ha- this just happened to me about a week ago - one of my chilli seeds sprouted with 3 coytledon leaves...i thought it was pretty weird aswell

When you folks see three cotyledons, is it followed by true leaves that come in threes as well?

I've currently got a basil plant that sprouted with 3 cotyledons (definitely 1 on one side and 2 on the other), and there seem to be 3 itty-bitty true leaves as well. Only time will tell whether the side branches follow suit.

Linda