I held off of going to the next era (from the first one) to get the legacy bonus. I had enough population to do so. When I got enough tech points for it, it let me select one of 3 choices but did not give me the stats for it. picked farmers, and the game said it was completed. I then, during the same turn, choose to become Babylon. This moved me to the next era, but did not give me the legacy bonus that was unlocked. It says it was completed on the turn, but after that turn it said it was never completed. I think the game is moving to the next era  before processing that the 10 tech points for the legacy bonus was completed, then not recording that the legacy bonus was completed that turn snice it is running under the new rules of the next era.

Has anyone else found this problem?

The same just happened to me. It did not matter which legacy bonus I chose.

I had the same issue

Had made a post about this

https://www.games2gether.com/amplitude-studios/humankind/forums/171-bug-reports/threads/38037-neolithic-era-legacy-trait?page=1#post-307496

Turns out they do work, but you can't see the trait listed, just its effect, and since the event doesn't tell you what each trait does...