This happened to me multiple times this year flying PHX-BUR via Mesa CJ-900. Basically the reason is that they evidently were not sure if the actual A/C flying that route on that day had an FC cabin or not. A few times I actually had an FC upgrade clear only to find no such cabin existed on the day of my flight which put me in the same row and seat but in a coach layout and a couple of times I never had the upgrade clear in advance but cleared day of departure when the aircraft servicing the route ended up having a FC cabin.

A lot of Mesa C-900 are getting new AA paint right now which appears to be throwing a wrench in scheduling.