Go to each application and look at "global permissions". That will tell you what user groups are considered administrators. It's quite likely that your current setup says to use the same group(s) for both applications. Add a new group for separate admins, put the admins in it, and apply it to the application you want to separate off, then, finally, remove the shared group from the global permission.
You must be using Crowd for User Management. https://confluence.atlassian.com/pages/viewpage.action?pageId=154046
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