The most typical reason is that your web server and WP CLI use different PHP runtimes. Then, for example, if you have Object Cache enabled web server might have proper access to it, but command line PHP might not.
This can create various out of sync kinks, if I remember right WP CLI have added checks that straight disable some functions for some of such scenarios.
Of course it’s just a general guess, which might not be your case. Practical troubleshooting would involve dumping the related data (such as value of related options and transient cache entries) in both contexts.