There's strong indication of a bug with patches for disc based games.
PSN download games seemed to update without problems, however, for my disc based games, which I didn't update for quite a while, there were problems installing the auto-downloaded patch.
It happened with Uncharted 3, Gran Turismo 5 and another game. So far, the disc based patches doesn't seem to work.
The problem may be because of multiple patches trying to be installed in the wrong order (from last to first instead of first to last). For uncharted, I can say the the last patch tries to install, it goes to 100%, and then it gives an error on the smaller patch (its size can be seen but the error is given at 0%.)
If you try to patch with the game disc booted, it tries to install the auto-downloaded patch, and it gives the same error. To be able to patch, you need to DELETE the auto-downloaded patch first.
When starting the game and downloading the patches manually, the smaller patch is downloaded first and installed, which makes me think the patches in the auto-download is not applied in the correct order.
Please consider this as a bug report, please let me know if this is a known issue or if there's a solution to it, or otherwise let this be a bug report for the PSN team.