When you deploy more than one JSF application and then you undeploy one of them, you'll face following message in server log:

SEVERE [javax.faces] (MSC service thread 1-2) Unable to obtain InjectionProvider from init time FacesContext. Does this container implement the Mojarra Injection SPI?
SEVERE [javax.faces] (MSC service thread 1-2) Unable to call @PreDestroy annotated methods because no InjectionProvider can be found. Does this container implement the Mojarra Injection SPI?

I think javax.faces.FactoryFinder.FactoryManagerCache.getApplicationFactoryManager(ClassLoader) shouldn't try to create new instance of FactoryManager in this case. I am not really sure, what is special initialization case, but it seems to me that this should evaluate to true in this case (btw Does this javax.faces.FactoryFinder.FactoryManagerCache.detectSpecialInitializationCase(FacesContext) ever evaluate as true?).