Gore-Tex technology is highly-efficient and amazing, but it is certainly not perfect. Just like anything else, there may be times where your Gore-Tex pants succumb to abrasions, holes, and general damage. Even if the fabric is resistant to them, it can still happen. Thankfully, depending on the extent of the damage, you can patch certain abrasions and holes. If it is too large, you may be out of luck. However, you can find repair kits at certain specialty stores. Or, you can order it online.
What you get with this kit are adhesive patches that will provide you an instant fix to maintain the integrity of the fabric. After all, if they allow water inside they kind of lose their purpose. For a more long-term solution, you can also contact Gore themselves as they will give you all the information you need about contacting a repair center.