Installing FIM hotfix FIMService_x64_KB3048056 fails

I tried to install FIM hotfix for service and portal, FIMService_x64_KB3048056. It just fails. Using msiexec I managed to get an log file which says this:

System.Reflection.TargetInvocationException: Exception has been thrown by the target of an invocation. ---> System.IO.FileNotFoundException: The Web application at http://sp.site.net could not be found. Verify that you have typed the URL correctly. If the URL should be serving existing content, the system administrator may need to add a new request URL mapping to the intended application.
   at Microsoft.SharePoint.SPSite.LookupSiteInfo(SPFarm farm, Boolean contextSite, Boolean swapSchemeForPathBasedSites, Uri& requestUri, Boolean& lookupRequiredContext, Guid& applicationId, Guid& contentDatabaseId, Guid& siteId, Guid& siteSubscriptionId, SPUrlZone& zone, String& serverRelativeUrl, Boolean& hostHeaderIsSiteName, Boolean& appWebRequest, String& appHostHeaderRedirectDomain, String& appSiteDomainPrefix, String& subscriptionName, String& appSiteDomainId, Uri& primaryUri)
   at Microsoft.SharePoint.SPSite..ctor(SPFarm farm, Uri requestUri, Boolean contextSite, Boolean swapSchemeForPathBasedSites, SPUserToken userToken)
   at Microsoft.SharePoint.SPSite..ctor(SPFarm farm, Uri requestUri, Boolean contextSite, SPUserToken userToken)
   at Microsoft.SharePoint.SPSite..ctor(String requestUrl)
   at Microsoft.IdentityManagement.ManagedCustomActions.SharepointCustomActions.VerifyClaimsAuthenticationOff(Session session)
   --- End of inner exception stack trace ---
   at System.RuntimeMethodHandle.InvokeMethod(Object target, Object arguments, Signature sig, Boolean constructor)
   at System.Reflection.RuntimeMethodInfo.UnsafeInvokeInternal(Object obj, Object parameters, Object arguments)
   at System.Reflection.RuntimeMethodInfo.Invoke(Object obj, BindingFlags invokeAttr, Binder binder, Object parameters, CultureInfo culture)
   at Microsoft.Deployment.WindowsInstaller.CustomActionProxy.InvokeCustomAction(Int32 sessionHandle, String entryPoint, IntPtr remotingDelegatePtr)
CustomAction VerifySharePoint2013ClaimsAuthenticationOff returned actual error code 1603 (note this may not be 100% accurate if translation happened inside sandbox)