Note: I was having the same problem. If you just keep pressing the upgrade button it will continue where it left off and eventually it will finish.
I think the problem is that those errors make the script take a long time to finish, and if you have a shitty server (my shitty server is run by Dreamhost.com) then you end up wasting your 30 second limit and the script just stops, so you have to manually restart it.
My problem now is that once the whole thing is finished my term_relationships are all fucked up and months worth are missing.
One solution I found was to export my DB using phpmyadmin, upgrade it inside a local wp install on my laptop (i use MAMP on mac, XAMPP is the same thing on windows), which only took like 1 second instead of 2 mintues. Then I just exported the database and imported it back into my original db. Not very efficient and pretty dangerous but stuck is stuck.