The body of elders that I was a part of, in Texas BTW, was a marking machine. It was a regular feature and I have personally talked to the service desk in NY regarding the "proper protocol".
The most common marking is for those dating or marrying unbelievers. But it can apply to almost any situation and is at the discretion of the elder body for anything that is not technically a disfellowshipping matter but would represent shady conduct. By the protocol outlined from WT, the person is to be counseled first. If they don't respond and continue with their course then they would be informed that they are going to be marked.
This takes place with a talk from the platform where the person is not specifically identified, but the congo is given specific enough info to get the idea of whom and why. For instance, 'Would we want to associate with one who flaunts righteous standards by dating a worldly man...' or 'We should guard against association with ones who would be involved with (fill in the blank)', etc.
paul