One of the leading causes of holes in these leaves is a little pest called the leaf-mining fly, or Liriomyza melanogaster. It lives in the soil by day and comes out at night to do its dirty work.
A host of other insects and critters can chew on your Pothos, too, causing holes. Many are only found outdoors and will attack your plant if you set it outside in the summer.
Bacterial and fungal diseases are one of the most common reasons for leaf holes in Pothos. They can infect the leaves, kill the leaf tissue and cause lesions that turn into holes.