It doesn't happen when the battle first starts, but once the NPC switches in a new Pokemon its Ability might activate twice.
Some of abilities that are affected are Intimidate, Unnerve, Mold Breaker, Turboblaze, Forewarn, and Frisk. This seems to happen with Abilities that activate when the Pokemon switches in.
One thing to note is that Forewarn alerted Musharna of two different moves when this happened, Crunch and Dig, suggesting that the abilities are actually activating twice rather than just displaying the message twice. Also, Trace and Drought did not display a second message likely because Drought cannot replace sunlight and Trace was already replaced the first time.
"Steve sent out Hawlucha!
Hawlucha breaks the mold!
Hawlucha breaks the mold!
What will Arcanine do?"
How to reproduce:
1) Create an NPC trainer with the NPC editor
2) Set the first Pokemon to be any Pokemon (lets say Rattata)
3) Set the second Pokemon to be a Pokemon with one of the affected Abilities (lets say Intimidate Arcanine)
4) Challenge the Trainer to a battle.
5) Defeat the first Pokemon.
6) When the Trainer sends out their second Pokemon with the affected Ability, the Ability should activate twice.
Tested on the Pixelmon Modpack on Curseforge.