Embroidery can be used to fix patch over holes. Embroidery can also be done over stains to hide the marks and make a feature. I did this with my daughters school shirt. I did white lazy daisies over stains on the white t-shirt, completely hiding the stain and the daisies blending in with the shirt.
There are some great embroidery stitching techniques that can be used to cover over holes and tears. Stiches described in 10 Hand Embroidery Stitches are good to use to sew over holes such as:
- Lazy Daisy chain flowers
- Satin stitch
- French knots
This video gives some great suggestions on how you can use embroidery to cover over holes and there are many others out there: