Are you talking about the dust boot? Most calipers have an external dust boot that prevents dirt and water from contacting the square o-ring seal. The seal is down in the piston bore, captured between a grove in the caliper body and the piston, so there's no way for any part of the brake pad to make contact with the actual seal.
Now, if the dust boot is damaged, it should be replaced and they're a couple bucks at any auto parts store. Is it possible that you're just seeing assembly lube leaking from the dust boot? Sometimes it's a grease, others they just use brake fluid in place of actual assembly lube.
Welcome to CB.com...first post. Woo-hoo!