The crystal creatures are technically fully functional organisms themselves but they're also a part of a much larger organism. The Jeweled Mountains are a living thing. Well, more of a collection of many living things that make up one body. The creatures are trying to rid the body of foreign objects. They're somewhat akin to antibodies. But if antibodies were kind of like bees.
The mere presence of foreign objects isn't enough to alert the creatures. But when those objects stay around for an extended period of time and disturb the environment around them, it's enough for the creatures to come running. It's not just extraplanetary objects or beings that trigger this response, if an organism from another part of Anide 1 were to make the mistake of staying around for too long it would be attacked as well.
The shuttle caught the creature's curiosity, and if nothing else, they're very thorough in eliminating threats to the Jeweled Mountains' health. Izzy's got her work cut out for her here.