Oh yes, this is definately a deviation from the protocol.
From you description, the protocol states that all equipment must be tested and, due to operator error, 3 critical items were missed. That is a deviation from the protocol. Deviations must be raised for this, so that the problem can be resolved (by repeating the relevant sections of the protocol?).
A note must be made in the relevant section of the protocol that “deviation XX was raised due to swabs and rinse water tests being missed on equipment zzzz, aaa & bbbb due to operator error” … or words to that effect. If you do not record that the swabs were missed AND a deviation was raised because of this, this would be a serious GMP non-compliance.
I hope this answers your question. Remember, any test stated in the protocol, which has not been done exactly as stated in the protocol will need to have a deviation raised for it.