no worries, I've had the same thing happen with the 3 piece air lock and the s type. you're fine it won't affect your batch. It happens when the carboy cools down. it creates a vacuum in the carboy and suck in a little. the big thing with this is it means you are getting temperature fluctuations in your fermentation temp which may not be the best for your yeast when it comes to off flavors. a spare refrigerator with a temp control for your fermenters would be a good investment to hold your temps steady.
the "s" type seems to be more forgiving when it comes to sucking in fluids but you could still suck in air past it which be bad. you really don't want air in your fermenter after your fermentation has started past the 12 hour point...