Hi. I logged in on 11/14 and noted after I completed my daily challenges that my Challenge Journal did not reset but still showed the challenges I completed on 11/13 and I did not receive the Marks of Favors for the challenges I completed that day other than the 1200 for the 6 upgrades I completed and 100 monster kills. Is there any way to remedy this and has this happened to anyone else?
Obvious question: you didn’t log in on the 14th before they reset? 
The Lockout Timers window (shift+L) shows you exactly when your daily challenges reset. Depending on your time zone that might be in the middle of the day.
The timer rest, but the challenges didn’t.
I have 19 hours and 13 minutes left on my timer as of this post (11:45 UTC). If yours reset 8+ hours ago (based on the time of your post), it looks like there’s something wrong with the timer on your end. Is your system clock and time zone set correctly?
It appears to be working now. This happened just before the Dark Agartha update. Maybe that messed with it?