Is manaphy malfunctioning?

ItzLuckess

My opponent used boss order on my manaphy and was able to use greninja to hit my bench.

TheRisingUnited

Manaphy only protects the bench from damage that are not placed by damage counters

TheRisingUnited

There also might have been an item card or stadium card in play that cancels abilities

Ravenclawed1234

Or a Pokémon

TechHog

Did the opponent use Cancelling Cologne?