Now before anyone says "No one can help you with that" please understand that the upgrade worked, this is just a weird bug.
Ok so I upgraded Joomla from 2.5.14 successfully and everything works, nothing out of the ordinary. Every component/module/plugin seems to be working as it should.
HOWEVER the extension manager has a strange behavior, it constantly says:
-1 Copy file failed
I would think file permission problems, but everything is writable. The wierdest thing is it actually installed perfectly, just get this error rather then it saying it worked. (Meaning that when I install the component, there is no error).
This also only happens with components.
Just strange, might be worthy of diving deeper into it in case others run into this with an upgrade. I do not know enough about how the extension manager works to try to identify the problem either, and the lack of a real (or accurate) error message makes it even harder. (the files did copy, so that error message seems out of place)
I will try to look a little deeper in it and see if I cannot isolate it, For those who want to try to recreate it, you can do it by upgrading from 2.5.14 to 3.1.5 though the update manager. The main components I have are no number extension manager, akeeba and admin tools that I feel might have something to do with it.
That most likely is a permissions issue. That error is a RuntimeException thrown by the JFolder class method copy() while trying to copy a file into a folder - src_folder/file to dest_folder/file.
Check your FTP settings in global configuration and then the directories permissions.