Hi @ramon,
For DOIs, by using DOI plugin and clicking “Assign DOIs,” this, in effect, will give anything a DOI that doesn’t have one a DOI, which, I believe, may have led to the situation that you’re in. If you only want to activate DOIs for specific issues, it is best to do this at the article level. This post goes into a little more detail on how to do that: DOI Assignment at Submission Level: A Question
I should note that work around this is planned for 3.4, that should hopefully make it easy to assign DOIs “bulk actions” but right now if you’re trying to just hit a few without assigning DOIs to all your content, it is best to do this individually.
-Roger
PKP Team