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I’m also experiencing the same issue with Fences S6.20 (ja-JP), which I purchased on Steam.
In my setup, this occurs when the “Roll-up” feature is enabled.
It appears that this problem arises because when a roll-up is closed, the folder within the Fence remains selected even though it’s hidden.
It seems that if you select or double-click a folder inside a Fence with the Rollup feature enabled, and then rename the folder or file on the desktop, the folder inside the Fence—which remains selected—will also be renamed simultaneously.
You can avoid this renaming bug by clicking on an empty area of the desktop before renaming, which deselects the folder inside the Fence that is currently hidden, but this workaround is very cumbersome.