I ran into the same issue while trying the same thing as Web-Beest.
How did you end up solving/bypassing this issue?
@tim-diels, I am running into the same issues.
This issue occurs when I am cloning a taxonomy term.
The taxonomy in question has an "Entity reference revisions" field to add paragraphs to the terms.
One of these paragraphs has an "Entity reference" field to reference nodes, this is where I run into the described issue.
When I edit the referenced node on the cloned taxonomy term (no checkboxes checked), the referenced node on the original term changes as well.