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That definitely sounds like a bug. I think at one point it was the other way around (where modules left out of the .cabal file but referenced by source files wouldn't get loaded), but this is going a bit too far :)
Does running stack build and then stack ghci again help? In theory, the stack build should refresh the interface files and remove mentions of the removed module. Although stack ghci should be running the build first anyway, unless you're passing in --no-build.
Yup, that explains it! Perhaps for the GHCI case we could have it skip any unlisted module which can't be found on the file system. In any case, we could make the warning in case of failed pre-GHCi build more clear that there can be inconsistent results.