I've reproduced. It looks to me like this code tries to canonicalize the path from the current directory rather than from the package's root directory. So if you do cd original; stack test --pedantic it will show the fully qualified path as expected.
I have a package in the subdirectory 'original/'. A compiler warning mentions a file in that package, Mechanism.hs. However, it's listed as "src/Mechanism.hs", not "original/src/Mechanism.hs":
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