It is one of those annoying "ICE validations", which sometimes have no practical value whatsoever.
You can managed it by disabling ICE validation via Light.exe command line arguments. Providing the runtime behavior of your MSI is still OK.
Alternatively you can just inject "RemoveFile" XML element where MSI wants it to be.
The starting point would be to set project.PreserveTempFiles = true; and analyse the produced .wxs file. If you can see what adjustments your WiX XML requires you can make them on fly (see InjectXML sample).
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You can managed it by disabling ICE validation via Light.exe command line arguments. Providing the runtime behavior of your MSI is still OK.
Alternatively you can just inject "RemoveFile" XML element where MSI wants it to be.
The starting point would be to set project.PreserveTempFiles = true; and analyse the produced .wxs file. If you can see what adjustments your WiX XML requires you can make them on fly (see InjectXML sample).
.