It's not a huge problem, but its very concerning that a program used to manage files is getting out of sync like this, makes me wonder if more is going on behind the scenes.
I have seen exactly the same problem. I don't know any way to reproduce it, but it does seem to happen after a lister with several tabs has been open for many hours without any interaction by me with the lister (for example, overnight), although there may have been changes to the files showing in the lister. It probably happens about once a week. Closing the lister and starting a new one fixes it, so not exactly a major problem. If there is any evidence I can capture next time it happens, let me know.