This happens a fair bit, and not just in connection with ghc-mod although it's the most common culprit. While doing the training at LambdaConf we had a beginner get very confused because their system installed GHC was pre-FTP and the Stack provided GHC was 7.10.3. From there, they didn't understand ghci and stack ghci would be from substantially different versions of GHC.

I'd really like Stack to stop implicitly using system-installed versions of GHC without explicit direction from the user.