this is correct. you cannot modify the contents of a vApp in a catalog directly in the way you want.
In vCD 5.1.x, you would deploy a copy ... make appropriate changes (delete VMs) ... capture to catalog under a different name.
In vCD 5.5.x, there is a second path.
you would deploy a copy ... make appropriate changes (delete VMs) ... capture to catalog under the same name, replacing the previous instance (this increases the version displayed by 1).