We have JIRA 6.2.5 integrated with Stash.

I had disabled the Keyboard Shortcuts Plugin in Stash, with the intent of preventing users from accidentally approving Pull Requests. As a result, when a user clicked on the 'Create Branch' link in JIRA, it would take them to Stash and they would see the Skull & Crossbones "Contact your system admin" error.

I looked at the atlassian-stash.log in the stash home directory and found the following:

2014-10-09 11:55:01,921 ERROR [http-bio-7990-exec-4407] 715x6219402x0 1iq1m3f 192.168.27.97 "GET /mvc/error500 HTTP/1.1" c.a.s.i.web.ErrorPageController There was an unhandled error loading [/plugins/servlet/create-branch]
2014-10-09 11:55:01,966 WARN  [http-bio-7990-exec-4407] 715x6219402x0 1iq1m3f 192.168.27.97 "GET /mvc/error500 HTTP/1.1" c.a.p.w.DefaultResourceDependencyResolver Cannot include disabled web resource module: com

The only change I made to Stash recently was disabling this plugin, so I tried reenabling it, and the problem went away. It looks like theres some dependency on the plugin for creating a new branch (at least in the versions I'm using)