We found root cost for this issue. Our project contains many *.config files which in majority cases should be copied to target directories. And therefore they are configured as "content" and <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>. To avoid listing and redefining every single config file in project which this attributes we added following config to project.
<Content Include="***.config">
<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
</Content>
Based on Microsoft SDK style project documentation. By default obj and bin folder are excluded from this rules (https://learn.microsoft.com/en-us/dotnet/core/project-sdk/overview). However when such project is loaded over Microsoft.Build.Evaluation.Project fthose files will be listed as project item with Content\PreserveNewest as this class is ignoring DefaultItemExcludes locations and therefore files are incorrectly considered as content of project files. We will be raising bug for Microsoft.Build.Evaluation.