This question is in reference to Atlassian Documentation: Configuring columns
From the documentation:
However, some statuses (in particular, custom statuses) may not be available for issues on your board if the JIRA workflowsused by these issues do not utilize those statuses.
No, you've not misunderstood it, but Atlassian (and frankly most of us administrators) have had support issues where people have said "my column is empty" or "I can't drag anything into the column" and it's turned out to be because the column doesn't contain any status or it has a status in it that is not used in the project(s) the board is looking at.
Some people do add columns that will be empty, but it's more likely to happen when a board is reconfigured and drops a project out, and that's the only project using a status.
So, on to your missing issues - can you find one to experiment with and check that it's in the sprint as well as in the right status? If it's a Kanban board, also check the fix version field is empty.
Good, that rules out a few things. Some further questions now you've narrowed it down loads:
Edit - oops, sorry, a screenshot of the column config screen might be handy too.
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