Currently there is not possible to filter groups for application.
One example where this may be useful: when using nested groups. I want to use group1 to give access to confluence space. But group1 has subgroup group2 where user belongs. So in order to authenticate with confluence I have to pull to crowd both group1 and group2 and add them to confluence application groups list in Crowd. But now administrator can see 2 groups in confluence: group1 and group2 and that may be question fro another administrator who does not know which group he/she should select. So It would be useful to have a feature where crowd administrator can select which groups confluence application is allowed to see.