I believe we have a fix for this internally already, just waiting to be verified. I'd expect it to be patched next week.

It's incorrectly requiring at least 1 corruption for the 1st kill to count (which can be seen in your screenshot too in the top right corner of the UI), so if you re-kill the Harbinger in Empowereds or by increasing the corruption of the level 90 timeline it will count.

The Crest not working is a consequence/second part of this bug. If you're at 0/10 in the Faction panel (as the level 90 Timeline kill didn't count), the Crest doesn't allow you to block the spawn because you didn't have the correct (incorrect) requirement of 1 Corruption for the first Harbinger to get to 1/10.

Once you have gotten through this weird state of 0/10 and are in the correct state of 1/10 of completed Harbingers as you should when you kill the level 90 Timeline Harbinger for the first time, then the Crest should work and allow you to block the HBs from spawning.

Just like any other Timeline, you can increase the corruption of a level 90 Timeline by killing a Shade in that Timeline to meet the minimum corruption requirement of 1 to have an easier fight. This then gets you to the correct 1/10 state in the Faction and the Crest should allow you to prevent Harbingers from spawning. Hope this helps, and sorry for the bug!

It should, since you're still in that weird 0/10 state with the Faction. If that doesn't work, you can also try another 90 Timeline with at least 1 corruption.