What issues were there? Usually when this happens it's because someone either uploaded the whole /upload/ folder instead of the contents, or else they uploaded the contents to the wrong place, only upoaded part of the contents or possibly used incorrect FTP transfer settings (should be merge folders)
It's more or less the same exact process as xf1 apart from the simpler process in the Addons section of the ACP.
For instance, it says in the instructions linked to above:
Once the files are uploaded, in the XenForo control panel, go to the Add-ons section. The add-on you just uploaded should be listed as installable or upgradeable. Click the relevant button and follow the on-screen instructions.