Clean the surface around the hole by rubbing it with a fine grit sandpaper. The sandpaper will also roughen up the area and help the acrylic putty to stick.
Fill the hole with an acrylic putty using a putty knife. Spread the putty using the knife at a low angle to the surface. Remove excess putty by holding the knife at more of an angle. Ensure that you completely fill the hole and feather the putty smoothly around the edges of the hole. Allow the putty to dry according to the directions on the package.
Sand the repaired area lightly with a fine grit sandpaper. Smooth off any bumps or ridges so that the dried putty is as smooth as the area around it.
Paint the repaired area with an acrylic spray paint that matches the color of the liner. Hold the spray can 6 to 8 inches from the surface and apply the paint in short bursts as you move the can horizontally over the area. Allow the paint to dry for the amount of time specified by the paint manufacturer before using the shower.