Hi Tim,
Yes, sadly, this is normal behaviour. NCrunch needs to watch the directories of all dependencies to pick up on file system changes .. and this has a side-effect of locking them at root.
Best practice is to always disable NCrunch when performing Nuget updates. This is because the way in which Nuget updates project files and references can cause consistency issues that make the engine desync from the foreground solution. If the engine is disabled, the packages directory will unlocked.