What I think is happening, is that the client is copying an existing SKU item in the CMS (which in my case creates 3 records in COM_SKU, I think one per enabled language variant I have), and then later deletes it. The COM_SKU records are left behind, but the CMS_Tree record gets removed?
Is this expected behaviour? I can of course write a script to remove any orphaned records, but I feel this might keep happening.