A tags blog's long URLs all point to the originating blog's post URLs, even though the individual posts are imported into the tags blog posts table and are editable there. But Yourls is generating a second short URL that points to the post stored in the tags blog domain database table, not the originating blog domain database tables. This seems like it would cause duplicate content issues.
At any rate, the generation of a second short URL is doubling the number of URL pointers being used. Additionally, it sends two tweets, each containing a different short URL that go to the same content but on different blogs.
The original short URL is put into the original post content, so if I could think of a way to have Yourls look for it and, if present, not generate another and use the existing one instead (the duplicate is inserted into the tags blog post in place of the original), I would try it out.
As a debugging step, I network deactivated Yourls and activated individually on all blogs except the tags blog. But that is how I had it set way back when I had the tags blog unsearchable by spiders and it still generated duplicates; making me wonder how it found the posts to generate URLs for.