In Ghanaian English, protocol is the use of a personal connection to obtain something that is meant to be allocated on merit or by queue: a hospital bed, a school admission, a passport appointment, a national service posting to a particular office.
“He went by protocol” is not a compliment, and it is not quite an accusation either. It describes how a great many things in Ghana actually move, and the same person will condemn it on Monday and use it on Friday.
Two honest things to know. It is real, and pretending it is not will leave you waiting behind people who are not waiting. And it is not a substitute for the requirements - protocol moves you up a queue, it does not conjure a document you do not have, and anyone offering the second is selling you a fraud.