Her insecurities could be reflected in the manner that she thinks she is ugly. Sometimes when someone projects feelings like these, there is a deeper meaning for their emotions. The roots may go much father then you think. Sometimes it can even be due to how they have been brought up or how others react to them. Unfortunately these things cannot be undone, but there is some possible methods you could take.
If she seems to be fixated on how she looks or appears to other people that is one singular thing. If she is stressing over even small things, like her manerisms around people, perhaps the way she moves or what she says in conversation in is deffiently deep rooted insercurities.
One method you can consider is to boost her confidence in otehr areas. Everyone at least likes one part of themselves. Weither it be their hair or lips, eyes, nose, legs etc. Its very difficult for this day and age as women because standards are much higher in regards to physical apperance. There are many workshops now for young girls to save their independence from the media and otehr forms of pressure. Reassure her no one is perfect and to appriciate what she has to offer.
The way you talk to one another or others around you can also effect the way she might percieve herself. If you are always constantly judgeing others (which all young girls do for some strange reason) just remember someone might harness that negativity and that night cause some insecurities too.
Try to focus on the positive and what you both enjoy. It will be fine. What you’re doing now is good. I also agree with sandpiper with how we percieve our selves is different from other. We may appeared warped or ugly in this case even though everyone eles sees a wonderful person. I have been guilty of it myself and even been considered to have it. I have been down the same road thinking I was repulsive and shouldnt look anyone in the eye. It comes with growth and tolerance. Just never turn away and be ther for her