Weird. Did you have no errors in your logs? Possibly an upgrade script or two was timing out?
From the looks of it, 4.0.23-4.0.24 upgrade scripts contained a large number of queries designed to improve performance of various MySQL tables. It is possible that if you have a sufficiently large database and/or the targeted tables contained a large amount of data, then those changes could take a long time and potentially not complete before the 15-second AJAX timeout on the install page (you might see relevant "slow queries" in your logs). If that is all that happened, then I think it should be fine. The scripts were acknowledging those MySQL tables as potential sources of slow queries and attempting to improve them.