Multiple entries for a URL may appear in the Yourls database. This is due to a concurrency issue with the yourls-api. This has already been reported by a user to the yourls forum.
Note (Before activating Yourls as your preferred shortener):
Add an entry for your WordPress blog homepage. This will prevent your page from freezing on first load as yourls-api would be able to return the shortened URL version without going into a request loop.
Shortcodes
Not all services may work with the shortcode.
However, non-login services are definitely working.
Snipurl / Snurl / Sn.im / Cl.lk / Snipr
There seems to be an issue with their API sometimes which doesn't allow URLs to be shortened
Even the example in the API documentation is not working.
However, I've included a workaround for it which hopefully will work persistently.