When you encounter this error, it's because you can't use a masking set that has multiple rule controllers with SQL Clone's imaging workflow currently. This is documented here.
The workaround is normally to put each Rule Controller into its own separate masking set and supply each as a separate file to SQL Clone in the web UI.
If you are using the Powershell, bellow is a sample script to do it:
$mask1 = New-SqlCloneMask -Path \\red-gate\masking-sets\production1.DMSMaskSet
$mask2 = New-SqlCloneMask -Path \\red-gate\masking-sets\production2.DMSMaskSet
$mask3 = New-SqlCloneMask -Path \\red-gate\masking-sets\production3.DMSMaskSet
$ImageOperation = New-SqlCloneImage -Name $name `
-SqlServerInstance $SqlServer `
-BackupFileName @('\\red-gate\backups\AdventureWorks-201701012210.bak') `
-Destination $ImageDestination `
-Modifications @($mask1, $mask2,$mask3)