@florent I'm not sure what's going on, but the incorrect size warning seems to be intermittent now.
Jan 22nd - No size warning. Half of the VMs cleaned 1 unused VHD, the others had 0.
Jan 23rd - Size warning and 1 unused VHD cleaned on half of the VMs. Others had neither.
Jan 24th - Same as Jan 23rd.
Jan 25th - Size warning and 2 unused VHD cleaned on half of the VMs. Others had 1 unused VHD cleaned.
Jan 26th - No size warning. All VMs cleaned 1 unused VHD.
It doesn't seem host related as each host had VMs in both categories. Hope this helps. Let me know if you need any more info.