The easiest way to prevent this configuration issue is to only make changes to VLAN ports at either Group configuration level or the Individual configuration level - never both.
A more precise way to avoid this issue is to avoid making group updates to default elements in a list and then removing those elements from the router’s individual configuration. Instead, only make modifications to a default list's elements in a router's individual configuration. Alternatively, remove the default array elements from the group and add them back to the router’s individual configuration as needed.
How to fix a configuration that encounter this issue:
Modify the group configuration so the VLAN ports are reset to their default-configuration state.
Update the router’s individual configuration as necessary to override the VLAN ports and obtain the desired VLAN port configuration.