Matt, first off is she talking about getting a zit or hives or anaphylactic shock or what? Whatever she's referring to I don't see it as your fault. From what I have read it is a fallacy that certain foods (like chocolate) cause acne and if she is talking about some other type of reaction I don't think you could be blamed if she has neglected to tell you that she has a food allergy. I'm sure you were hurt by hearing this information by a back door instead of having her come to you directly. If you had any, throw that guilt right out the window.
I don't know what your arrangement is with your roommates so I'm not quite sure how to answer your question. Do you take turns cooking for one another on different nights? If that is the understanding then I'm sure it is also understood that anyone who lives there may sit down at the table and partake without being specifically invited every time. If you have made arrangements between you that you will take turns with the cooking then I think food preferences and allergies should be taken into consideration when it is your turn to do the cooking. If you have to cook to your audience you might make something different than you would make just to please yourself. If it's looser than that, like "Hey, I feel like making stuffed shells tonight and anybody who wants some is welcome to eat" then it is up to her to ask you how the dish was prepared or if it includes ingredients she wants to avoid.
Without knowing more about the situation I don't think you did anything wrong. You're too nice a person for that.
FWIW...Even if I did get a zit I would consider it a small price to pay for a delicious meal cooked for me by a friend...
When I stand before God at the end of my life, I would hope that I would not have a single bit of talent left and I could say “I used everything you gave me.”