Is this happening to anyone else? One supply route was sent to a settlement that had not even been discovered yet.

Today 3 more provisioners were sent off other settlements.

The version of the game is PC and the game is up to date, as well as heavily modded.

Yes similar thing has happened to me as well. Manually assigned 1 provisioner to the lighthouse. Next day, the game added 3 more routes to the same settlement.

Didn't really bother me too much though. I'm on ps4.

yeah i had that happen. i don't know of an easy way to fix your supply lines on console either. i had to run the provisioner down. took a lot more time than i wanted to spend.