I don't sell at Farmer's Markets but that does not surprise me. When you deal with people in public like that, you have to deal with all kinds of people. Asking for just two does not mean they have to be weird. In this economy, maybe twelve is a lot for them. Maybe they want to sample your eggs to see if they are going to be a regular customer. Maybe they have a recipe that calls for only two eggs. I've known people who would do something like that and never think a thing of it. Who knows why they asked for only two?
How you handle it is up to you. It may be too much of an inconvenience to you to break a dozen. Our systems are set up and it can be a pain to do something different. If you normally sell out, then you could easily lose a sale by not having a full dozen. There are plenty of legitimate reasons to not break a dozen.
If you do break it, you should charge a bit more per egg. I'd consider dividing the regular carton price by 12 to get the normal price per egg, then round up to a convenient number so I could avoid dealing with pennies. Say you charge $4.00 per dozen. $4.00/12 = $0.33, so charge $0.35 each, maybe $0.40 each, what ever you feel is right for you. It is extra inconvenience and probably extra work for you, so charging more is legitimate. If you provide special packaging, then it is even more justified.