Hi,
This warning is NCrunch telling you about something that is wrong with the dependency structure in your solution. It isn't necessarily an NCrunch problem - it can mess up many things in your build. There's a good chance that NCrunch will continue to work without obvious problems, though you'll be sitting on a timebomb that will almost certainly give you trouble at some stage.
Let's just say we have MyAssembly.dll which is a 3rd party dependency you've introduced from somewhere, and we have MyProject.csproj which has an assembly reference to MyAssembly.dll.
Now, we build MyProject.csproj. Normal build behaviour will copy MyAssembly.dll into MyProject's output directory, so it sits next to MyProject.dll.
Then, we go and delete MyAssembly.dll from the place where MyProject.csproj was originally referencing it. In normal circumstances, you would expect the build in this situation to be broken.
But it isn't. This is because MSBuild contains implicit behaviour that will search around for MyAssembly.dll in order to try and find it. Eventually, it will just settle on the copy of MyAssembly.dll in MyProject's build output directory, and use that instead.
This is dangerous because the contents of a build output directory should be transient and shouldn't be used as a source for assembly references, but MSBuild will do this if its primary search paths fail, and it won't warn you about it either .. but NCrunch will.
You should investigate how this file is being resolved and where it should be referenced from. Clearing out all your build output directories may help with troubleshooting this problem.