Soon you will receive a notice in the long service output if certain instances such as volumes get skipped because of the ‑‑exclude|‑X and ‑‑include|‑I switches.
./check_netapp_pro.pl Usage ‑H filer ‑o aggregate ‑X ^aggr0$ NETAPP OK - 2 aggregates checked. Max. used aggregate: aggr1 (12%). 1 instance has been skipped because of --include/--exclude settings. aggr1: 12% (OK) aggr2: 10% (OK) <| perfdata follows here>
This applies to all checks that can monitor multiple instances at once (overall checks).