I turned in the Cracked Keystone quest early in the week when I was not yet at the Gilded crest cap and I’m capped at 90/90 crests. Some others in my guild got to the Gilded crest cap and then turned it in later and are at 105/90. I believe the same thing happened with the 15 Runed crests. I don’t know if this was a mid-week change and has to do with when they turned it in or if they only ignored the cap if you were already at it, but this is clearly an unfair discrepancy.
I’m experiencing this as well. Also, I have done almost all bountiful delves this week and I’m not Delver’s journey rank 2.
A few other guildies aren’t even doing 11’s and are rank 2.
This needs to be fixed
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Any update Blizz? That’s pretty unfair for people like us at 90/90 while others are at 105/90… 
I don’t know why we’re pushing changes mid-week that result discrepancies like these. I know it’s a single item upgrade, but as I’m sure people are aware, gear means literally everything in these early weeks. Would hope for some form of compensation for the characters that have been screwed by this.
It’s now clear that I am in fact stuck 15 gilded crests behind.
On this character, which turned in the quest at the beginning of the week, I’m capped with 105 crests after having spent 75, so at a total of 180 crests.
On another character that turned in the quest later in the week, I’m at 27 gilded crests after spending 60 (a total of 87) but my progress toward the cap is 72/180, making it clear that the 15 crests from the quest didn’t count toward the cap.
Edit (August 24): I opened a ticket and got this response:
Regarding the quest and crests:
There was indeed a bug that was fixed. If players completed the quest while they were capped the crests were lost.
We looked into this but sadly it is not possible to hand out or compensate the crests to players that “missed” them before this was fixed.
I am really sorry aboutt his. I understand how annoying this is, especially at the start of the season, even if in the long run those few crests won’t make much difference.
So it’s a known issue and people who were affected just get to be permanently behind.
Edit #2 (August 25): I just logged in and got messages in chat (and mails from Thaumaturge Vashreen) saying that I got 15 gilded and 15 runed crests. I was briefly excited, thinking that they’d actually fixed the issue and compensated me properly, until I realized that the crests I was just “given” also counted against the cap and the actual number I received was 0.
Edit #3 (August 29): I just logged in and got the same messages and mail about getting the crests again, but this time I actually got them even though I was at the cap. So it seems they did finally manage to compensate people who lost out on those crests.
Still waiting for mine. Not sure how they are rolling it out, I could use that last 15 runed to get to achievement.