Just encounter a strange problem of key chain access. When prompting for access to credentials, the dialog can only be dismissed by Deny. In the console, “Ignoring user action since the dialog has received events from an untrusted source” was logged.
According to this post, 10.11.1 contains a security patch to prevent synthetic clicks on keychain dialogs. Try disabling all apps in the privacy settings of accessibility-mac-control, but not works.
Therefore manually quitting such apps one by one will be the trick to check for the culprit. It founds that BetterTouchTool is the problem.
Update: 10.11.5 will correctly prompt for administrator password and shows the blocking app.