CopyNativeDependencies is broken on Mono 3.4 at least. It works on 2.10.0 therefore it means something is broken.

LibGit2Sharp project doesn't use it, it uses a manual copy of the .targets file contents and it doesn't trigger any error.

It seems to be an invalid path issue, and it might be caused by trailing slashes. Any insight on how to debug?

See the following:
Tests csproj: https://github.com/libgit2/libgit2sharp/blob/vNext/LibGit2Sharp.Tests/LibGit2Sharp.Tests.csproj#L136
Targets file: https://github.com/libgit2/libgit2sharp/blob/vNext/LibGit2Sharp/CopyNativeDependencies.targets
Core csproj copy:
https://github.com/libgit2/libgit2sharp/blob/vNext/LibGit2Sharp/LibGit2Sharp.csproj#L334