Yep, have the same issue and filters have been set to target enemies only. And most the time they work just fine, except when there is a Carbuncle in the fight.
Can see it in action.....will be doing a FATE having no issues at all. Along comes an Arcanist with a Carbuncle, and suddenly there is targeting issues.

In proper format:

Targeting issue when there is a Carbuncle in the fight:

Time: whenever there is a Carbuncle in the fight
Frequency: always if there is a Carbuncle in fight
World name: Diabolos
Character name: Amelia Rose
NPC name: Carbuncle
Monster name: any
Class/Level: level 28 now, has been happening since coming into contact with Carbuncles.
Party or solo: FATE groups with a Carbuncle. Dungeons with a Carbuncle.
In-game time: any time
Area and coordinates: any place
Steps:
1. Find a FATE (can be already in progress)
2. Start trying to kill monsters by targeting them with (A) button.
3. If there is a Carbuncle present, the Carbuncle will automatically be selected.
4. If no Carbuncle is present, target selects monster ready to start killing it.

This is 100% repeatable

Controller: XBox PC Controller - wired.