I would inform the owner and the commissioner - same sitemail sent to both.
Like contrarian as a commissioner I have a league excel file.
One of the pages is 'Position Players,' another is 'Pitchers.' On it I copy and paste every player for a given season from the Draft Center. I'll project the players well into the future.
For instance, in the XYZ League, which is submitting keepers for the upcoming 1928/1978 season, I have all the players from 1927 thru 1939, 1977 thru 1989. The 1st two columns are blank. When a player is drafted I copy and paste the owner's name and team into those columns.
When keepers are submitted I check the owner's keeper post against his roster and will usually sitemail him if he missed someone. Most owners are very good about listing everyone, including cut and retired players, which helps a lot. Every season someone misses some player.
'Available Players' is another page in the excel workbook, and that's where I list all the players for the season by position. I delete the names of kept players from this sheet, use it to create the available players lists.
I usually cut owners and commissioners some slack when I notice a mistake. There are a lot of players to be accounted for in a 24-team league and it's easy to overlook a player or two.
Keeping track of what player belongs on what team does seem to be something that could be handled much better by the computer than by a human.