This has happened to me for quite some time already. I never bothered to report it as I can rely on the fact that raid tourneys begin from Monday to Friday at exactly 4:00 PM (Philippine Standard Time). I heavily rely on this fact for me to skip the raid chest for the second time of the day for me to fill it in, since I have a total of 11 flags (6 in regular raid flags and 5 in raid tourneys). This help me prepare for the 3rd raid chest to be skipped and fill sometime late in the evening.
All we can do is wait for it to get updated with the correct ranking. What matters the most is that the final score and ranking is correct at the end of the weekly raid tourney.