The standard response is:
(a) Submit a ticket to have the players replaced
(b) While waiting for that to happen, the owner should move those players to the minors so they don't appear in any games
(c) Team in question forfeits all games in which the ineligible players appeared
But if were in that league with you, I would not be happy about this. As commissioner, you've got to take a lot of responsibility here....you missed a 2000 Pedro Martinez? And you could have set up the league to only allow players from 1885-1985, thus making this much easier for you and preventing exactly this occurrence.