There are many creatures that will do this that fit the description of 'worms'.

They way to prevent it is to spray your plants with food safe insecticides regularly.

If you grow a lot of eggplant you can check the fruit weekly and immediately remove and destroy any with holes in it. Doing this improves undamaged yield over the long term according to one asian study.

There are alternatives to chemical sprays, but you have to play around with them to see what works for you. Diamatious earth spinkled around the plants and reapplied throughout the season may work out. Using neem oil products sprayed directly on the plants/fruit might work as well.

If you can get a picture of the pest posted a positive ID will help others in suggesting more specific control methods.