I also live in Chicago and use CityMapper almost exclusively now. It gives way more detailed estimates for multiple transfers between bus and train and generally comes up with more/better routes for weird destinations.
I think it’s a uniquely Chicago problem.
Here is an article on it: https://www.nbcchicago.com/news/local/cta-makes-more-changes...
I’ve personally also experienced the same issue with SF’s Muni.
As someone who has first hand experience with transit agencies, the tech infrastructure is unfortunately not to the level it should be.
That said, google isn’t always the easiest to communicate with when trying to fix such issues.