It means different things to different publications. The large one that I used to edit for used it to let other editors working that queue not to publish it.

It could have been image issues, citation issues, any host of things but they would leave PNs wherever there was an issue to let the writer know what needed to be fixed.

If there was/is a TK and nothing else then they suspect plagiarism and are drilling down on the submission to make sure it's on the up and up. If you remove a TK from en aditor you'll get an earful and rightfully so.