I have just ran the same tests as in the previous comment and confirm this bug seems to be resolved. I did it with Silents smaller box trap design and didn't get a second raid.
I am using the raid farm design from silentwisperer https://www.youtube.com/watch?v=LqvzA1Ripek&ab_channel=silentwisperer
The Bad Omen full screen pop up will trigger multiple times as both farms are going, how ever immediately after shutting the raid farms off I will drink a bucket of milk. This gets rid of my hero of the village effect and removes the icon in the top right corner, how ever there is no bad omen icon in the corner, and the effect still remains, I will wait 20 mins then go to a village trading hall and raids trigger.
As far as I can see Bad Omen no longer gives you two Bad Omens at once if you turn the raid farm off and make sure only one raid captain is killed, however if another raid captain is killed whilst a raid is active, you still get the invisible bad omen.