Hi Nick!
The yellow exclamation point means that the email address is associated with more than one contact and therefore MIST isn't sure where to put the message. As you noted, you have the contact personally and also for the church she does the missions work for. So that's where MIST is confused.
I realize MIST is making an assumption here: that you'd only want the email associated with ONE contact (hence this warning.) I've personally found that having information about people in two places leads to me missing stuff. However, would it be your preference to associate the email with both contacts? I could see that being helpful in some cases.
In either case, as a workaround, you could remove her email address from one contact, re-run that email through MIST, and then add it back. (You could do the same for the second contact if you'd like.)
Tom