Use a rag to rub warm water and isopropyl alcohol around the hole to clean off any dirt or grime. Let it dry for a few minutes before continuing. This will help the glue adhere to the rubber. Scrub the edges of the hole with sandpaper until it appears to take on a rougher texture. Remove the insole of the shoe and place a piece of duct tape inside the shoe where the hole is. If the hole does not go all the way through the inside of the shoe, put your finger in the hole and push up to see where the hole is and cover that part with duct tape. Being careful not to touch the adhesive with your bare hands, gently squeeze it into the hole. Make sure the entire hole is filled, and don’t worry if there is some overflow. The ice cube will allow you to smooth the surface of the glue without sticking to it. You can also use a tongue depressor or spoon covered with petroleum jelly. Set the shoe so that the sole is facing upwards. Leave it somewhere out of the way where it will be cool and dry. Leave it for at least a full day. Check to see if there is dried glue protruding from the hole or spilling out over the edges. If there is, use 120-grit sandpaper to sand it down until the bottom of the sole is smooth.

Summary:
Clean the area around the hole with water and alcohol. Roughen up the edges of the hole with 120-grit sandpaper. Put duct tape over the inside of the shoe above the hole. Fill the hole with shoe sole adhesive. Use an ice cube to smooth the surface of the adhesive. Let the shoe dry for 24 hours with the sole turned up. Sand down any dried adhesive that overflowed from the hole.