Recently Sharepoint Health analyzer on one of our FARM started showing the below error under section Missing server side dependencies.:
[MissingSetupFile] File [Features\NintexWorkflow\NintexCatalog\repair.aspx]
What We know is Content Database where site showing the error exists.
Note: We haven't installed the Nintex on this FARM but We transfer sites from UAT to Prod - vice versa & that farm has Nintex installed at some point of time in the past.
This content database had around 50 sites, we are not able to make it which site is causing the error so we researched a bit as there might be a SQL hack & we found it.
Credit to : http://justgeeks.blogspot.ie/2012/06/resolving-missing-references-when.html
Log on to the SQL server & query the DB in question:
select * from AllDocs where SetupPath like '%Features\NintexWorkflow\NintexCatalog\repair.aspx%'
As its a select query so I am not worried, running it on the SQL.
After the QUERY is run you will find the site in QUESTION, if its of no use you can just remove it from Central Administration.
Note:- Altering SQL for SharePoint is not supported so don't go that route.
What I have done is opened the site in Sharepoint designer & removed the ASPX file in question & than reanalyzed.
Issue disappeared on Our Farm, hope this troubleshooting will assist you as well in some way.