Perhaps this screenshot will help explain…
You’ll notice that the legendary gems I have are…
- Rank 25 Zei’s
- Rank 70 Bane of the Trapped
- Rank 25 Stricken
- Rank 11 Bane of the Powerful
- Rank 72 Whisper of Atonement
- Rank 99 Whisper of Atonement
The journey task was awarded completion when I levelled up the Bane of the Trapped from 69 to 70, with the two whispers already being higher than 70. If I’d obtained three whispers at 70 or above, the task would not have been marked off as completed. It’s the act of upgrading a gem to the right level, and the result of that upgrade being that you have three (or more) gems of that level, which triggers the task completion.
It’s not a bug.