I play f2p, and am on daily for hours. I never miss a check in, and e*ially not this month when i can obtain hibihime for free since I like to obtain every ninja possible.
Yesterday i checked in like normal and done everything, today when i went to check in it reverted yesterdays and no longer has it checked off, however it still has every day prior to yesterdays checked off.
If you could pull up a log to check users activities,etc it would verify i did indeed check in. Back when i was a developer for my game we had a system set in place to easily verify users situations such as these. "idk if you have something similar or not"
Hope can have some insight for this being able to be fixed