Ok, thanks for the quick response, makes sense. Sorry for not being clearer on my initial post, we have our code separated to shared library code, and then for each platform a project that has all the platform specific stuff (mostly just icons, layout and whatever is the startup). All tests and NCrunch relevant things are in their own test project just referencing the shared library code, so we don't care much about the platform specific projects as long as they compile. But this is exactly the issue, once NCrunch generates that extra file in the \obj\ folder the project won't longer compile unless that file is fixed or deleted. I also noticed today after changing it once and then deleting it, it gets generated correctly again.
We already use ignore the whole project, but I guess sometimes it is already loaded and stuff is generated and then causing the issue, not sure why it happened on the build system as the project was supposed to be ignored and looking at the metrics it is not there. For now it works fine, just next time we add an android or ios project it probably will pop up again, not worth the effort to write script, will fix it manually next time again, but would be nice in the future if nCrunch would not generate .Designer.cs files that don't compile.