Record exactly that: main equipment received, spare outstanding. Don't tick a box that says the whole ordered kit is present when it isn't. What does your receipt form actually say?
Ask purchasing to record the exception against the order and deal with that form. A comment in your maintenance notebook won't help if their system says everything was received
Has the seller agreed that the additional adapter is outstanding? We once had stores chasing a spare while sales believed the fitted item completed the quantity.