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There is the aptly named Non-Malicious Monster — a monstrous creature that is dangerous, violent, or destructive, but also is non-sapient has no concept of morality and is driven only by instinct or supernatural compulsion.
If they are sapient but have no notion of human morality, that's Blue-and-Orange Morality.
A quick Google image search suggests that these NASA monsters you mention could be Eldritch Abominations, which neatly collects all of this into one package: horrific, indiscriminately destructive creatures with their own inscrutable goals that you can only avoid or redirect rather than face head-on.
Horde of Alien Locusts may also apply in some cases. They're usually not unbeatable as single foes, but what are you going to do about the thousand others behind the one that died? And being so instinct- or hunger-driven means they are sometimes able to be pointed toward someone you don't like.
Edited by KD
Is there a trope for creatures or groups that are practically unbeatable, but obey their own set of rules, like being attracted to a magical beacon or fulfilling a prophecy. Thus, both sides of the conflict try to take advantage of it by having the non-malicious entity attack the other side?
I'm thinking in particular of the NASA monsters from The Adventures of Dr. McNinja, which kill anyone who attacks a NASA scientist regardless of context.