>>78656186His art style has never lent itself well to distinctive faces. His female faces are almost all pointed chins leading into rounded cheeks, while the male faces are usually square cheeks leading into a smaller square jaw. He differentiates in other features - hair and eye color, height, hair style, glasses, and piercings. He's pretty good about different clothing styles as well (see
http://questionablecontent.net/view.php?comic=3106 for a recent example of clothing and faces in a nice lineup).
Usually, this results in distinctive characters with a tendency for anime-like sameface. This time, he just made a few changes that didn't mesh well. They're both black haired, brown eyed women with no glasses or other distinguishing features. In the past, it hasn't been an issue, because Emily usually has a more distinct clothing style. Here, though, she isn't sporting the brightly colored dresses, and her hairstyle has changed, while Dora's new hairstyle is very, very close to Emily's old one.
He's made 3100+ comics, not every one's going to be perfect.