This is sorta similar to a previous thread I'd had between Brakus and Nekmo (which you can find here if you're so inclined).

Without fail, assuming there is nothing to kill, Rotos will always use his A2 against my Boragar over my Mortu. He'll use his A1 against Mortu, but not his A2. In fact, I just had this rather hilarious (only because I still ended up winning) interaction, where their Rotos got *five* extra turns due to relentless/A1. The moves went: A1 (against Mortu) - A2 (against Boragar) - A1 (against Mortu) - A3 (against Mortu) - A2 (against Boragar). At the end of that sequence, Mortu was at about 20% HP left, and Boragar was still at 100% - with his shield active, so Rotos gained zero HP out of that interaction. 

In terms of stats, Boragar has 90K HP and 3200 DEF, while Mortu has 81K HP and 2600 DEF. Boragar does have the most HP on my team - so I'd guess the AI is saying "target the person with the most HP". But that seems completely counter to how affinity matchups typically function - yes, Boragar has the most HP, but he's weak affinity for Rotos, while Mortu is strong affinity.