I was actually referring to trains being re-routed by the MTA -- like when the F was running on the E line in Manhattan a few weekends ago.

Ah. To be fair, I think all the apps do this now, including Google and Apple Maps.

Regarding alternate routes with Citymapper, I kind of wish it offered me alternates that don't necessarily include the original end station. I find I often end trips at stations I'm supposed to switch trains at and find routes to different stations than my initial route that still save time.