It sounds like you are close to having it right.
Basically with crowd licensing, 1 Crowd License Seat is defined as a user who can authenticate to 1 or more applications.
What you need to enusre is that only the groups you defined above for the variuos applications are the groups that are assigned to those applications and that under Directories in each Application, the allow all to authenticate is set to FALSE.
This means only the groups you specify for that application will allow those users to authenticate.
This will limit the number of users that crowd will calculate for its license count
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