The idea of export/import is to move/copy content from one OJS to another. If you have one issue on one OJS and one issue on other OJS, if you do export/import you want to have two issues on the other OJS. That is how it works. The same for articles.
The actual behaviour is, that the warning pops up and informs the user, that there is a duplicate, yes - but the issue gets added nevertheless as new dataset, so we have a duplicate (as of OJS 3.1.0.1).
This change should be in effect in 3.1.0-1, and the intent is to provide a warning that the issue identification was matched and to create a new issue only if one doesn’t exist. Any articles contained within the import’s issue would be created in the already existing issue. Can you share your XML import (or a snippet of your XML import) which causes the issue to be repeatedly duplicated?