Very early on, we found out that Bea is supposed to be mad at Alan but she doesn't remember what happened to anger her.
In recent pages, she found a letter that she wrote to Alan (http://thedreamercomic.com/comic.php?id=250) that includes "All I could think of was Milly Weaver gloating that you are Roxbury's finest dancer. And I could not help wondering if you have spent your summer dancing with her rather than writing me letters." On the next page, Alan refuses to explain who Milly Weaver is and Bea surmises that she is the reason she's supposed to be angry with him.
Did Alan do more than dance with her? I don't think we've gotten any more details yet.