I just logged in after waking up from a 7 hour sleep and joined a final boss checkpoint for Shattered Throne on my Hunter (this was the first dungeon OR raid content for this character since the Tuesday weekly reset) and I got zero credit for the commendations I gave to my teammates. I gave out both blue commendations and Giving Gratitude objective for Rank 9 did not change (continues to sit at 33/50).
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Same issue but there doing it on purpose to throttle how many commendations you can give, they added a timer so you have to wait for a certain amount of time