This behavior might be a result of the problem with incorrect configuration.
In Sitecore 8.2 there were some configuration changes. One of these changes is change in type attribute value of
<database> node. It has been changed from
"Sitecore.Data.Database, Sitecore.Kernel" to
I have seen the same behavior when I had a patch file that changed database nodes. My patch file also included database type value which did not match the new type. As a result, instead of patching new database node with the same ID was added.
/sitecore/admin/showconfig.axpx page to verify your configuration and ensure that you do not have the same problem.
If you figure out that the problem with configuration, you can simply search for the include file and remove type attribute and leave database id attribute only in
<database> node. This should be enough to apply the patch correctly.