I have an old intranet site running on 3.6.2 and tried to manually upgrade it to 4.1.1. After moving the files over the site just "spins". I have manually upgraded our sites literally 100 times (connection directly to wp.org does not work so there is no way to do it auto) and have never had this come up. I ended up going up one version at a time - 3.7, 3.8, 3.9, 4.0, 4.1) and this worked but wondering why it didn't take before?
Follow up question: Why can't wordpress recognize my version and then upgrade the DB appropriately?