This issue is related to the targets file here in the Windows ML samples: https://github.com/microsoft/WindowsAppSDK-Samples/blob/main/Samples/WindowsML/Resources/SqueezeNetModel.targets
The targets file leverages MSBuild's Copy task to ensure various dependencies make their way to the outputs of the WinML samples that need them.
From code inspection of the targets file below (h/t @Scottj1s), we should not be using this task, and instead leverage ItemGroup and None, either as entries in the individual project files or in a shared props file- which will give better predictability on ensuring these files land in the right places across all build scenarios.