NCrunch changes the build system so that your solution is built in pieces - one project at a time.
This involves considerable dependency management. NCrunch needs to be aware of every reference from a project at the time it loads this project, and it needs to be able to control how these dependencies are found by MSBuild at build time.
When working with a solution using a standard build with all the normal MSBuild targets, there are no problems. However, some frameworks use extensive build customisations or heavily altered logic that NCrunch hasn't been pre-programmed to be aware of. Sometimes the logic still follows the standard model closely enough that NCrunch is able to work with it, but in other cases the results are widely unpredictable. This makes it impossible to warrant how NCrunch will behave on unsupported projects like Azure.
In this particular case, it looks like the project being referenced by your Azure project is not a normal project type. Either it's placing an output DLL somewhere completely unconventional, or there is no actual physical output from the project. NCrunch is expecting to find an EXE or DLL output from this project, but when it looks, there is nothing.
If you'd like NCrunch to add support for Azure projects, you're
welcome to request this on uservoice.