Turn them inside out (only the jeans, leave the pockets as is).
Then sew and/or patch holes. You may need to cut or redesign the original pocket, possibly add extra fabric- all depending on how big the holes are.
Again, make sure you are repairing the pocket(s) with the jeans inside out, do not turn the pockets inside out, otherwise you will find yourself with pockets that have threading, patches, etc. in place where your hands or belongings would go. This may result in tearing open any repair you have made, and a good chance you would make extra holes, ultimately making the original pockets unrepairable.