No, the versions are project level items, and hence can be applied to any issue within the project.
You could implement some form of selective checking with validators, but you'll need some rules to decide what to apply to what, and some code to actually implement the checks.
You can solve this with Issue Type Screen Schemas (See https://confluence.atlassian.com/display/JIRA/Associating+Screen+and+Issue+Operation+Mappings+with+an+Issue+Type)
You just remove the Fix Version field from all screens associated with subtasks and Epics.
or, you can hide the field in a specific Field Configuration for the Issue Types in concern. See https://confluence.atlassian.com/display/JIRA/Specifying+Field+Behaviorfor more details.
With this approach you will get rid of the field entirely. In the first suggestion (with the screen scheme) you will still see the field but it is not editable
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