When the trigger is duplicated, the contents of its OnActorBeginOverlap MC delegate are copied, which contains a reference to the BP actor that added the binding to the original trigger.
Marking the property as 'duplicatetransient' is likely overkill, and it might break behavior that relies on this functionality. We may have to devise a custom solution here.
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To recreate this problem with the provided project:
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-161033 in the post.