I'm guessing at what's happening here .. but most archival tools work by assembling a copy of the data first and then they write that collection of data to the archive file. So if you have 2GB of original data on disk, the temp cache will also take 2GB and then you write the file (compressed) which is maybe 1.7GB, so you end up needing 3.7GB free on the disk to backup 2GB. Even if the final write is to a different disk (e.g. connected USB) you need 2GB on the original disk before it writes the 1.7GB to USB.
So I don't know how much data and free space you have on the USB stick, but most people running from a USB stick have small(er) capacities. The solution would be to stop kodi (systemctl stop kodi) and then recurcively copy files that you want to "back up" to another USB device, e.g. cp -R /storage/.kodi /some/other/device as the copy operation isn't assembling a grand copy of all data first.