I have been battling with this issue for weeks now, with help from Microsoft support and our SharePoint vendor as well. It isn't every file when this happens, but there is no indication as to why it happens in the first place. This is the setup.
SharePoint Online
Locally we use Office 2010
We have SharePoint online mapped to a drive for Windows Explorer view although it doesn't matter, upload failed happens on the website as well. The only two workarounds I have found without figuring out why this even happens is copying the file locally, then just copying it back to SharePoint Online and overwriting the same file. Also if we are in the website and use "excel/word online" it will work. Similarly Office 2013 has no issues.
This is the following things I have tried already with zero success.
Upload failed troubleshooting
Lowered all security settings in IE
Added Sharepoint sites to IE Trust sites
Repaired Office
Cleared Office Cache
Cleared Upload Cache
Removed all logins from Windows Vault
Removed Identity profiles from Regedit HKEY Office
Reinstalled Office 2010
Update Office (through windows update) and desktop software on the website.
Removed updates one by one checking to see if one was causing it.
Used Network Monitor to see any abnormalities when upload failed occurs.
Checked Event monitor in windows