@Shusternsk
1) If you have deployed an app to all users then it will be seen in App catalog for all users.
2) When any users install the app from App Catalog, the app is installed and the installation status is seen in the Software Center > Installation Status.
3) If you want the users not see the app in the software center then remove the app deployment for the users. Launch CM console > Click on Applications > select the app > at the bottom click on Deployments > right click the user group and click
Delete.
4) If you are still seeing the software on the users computer then wait for sometime else run the CM Client actions - http://prajwaldesai.com/configuration-manager-client-actions/