Soul Hackers 2

There’s two sets of Commander Skills; Active and Automatic, and all of them have to be triggered for the trophy. The Active Skills (Conversion, Master Conversion, Damage Condenser, Shield Deployment, Overlock and Stack Optimization) are used by pressing L1 when in combat (some battles - typically Aion Directives targets - may disable this), then select the one you want to use. You can only use 1 per turn, and they take a certain number of turns to “recharge.” Just go down the list, ticking them off.

The Automatic Skills are a little tricker. They have a chance to activate in combat when certain conditions are met. Most of them are fairly simple:

Auto-Repair: Let your team get beat up fairly badly. Triggers when several members are below 50% health, adds a health regen effect.

MP Optimization: Run down the team’s MP. Triggers when MP reserves are running low, cutting MP costs in half.

Turn Extension: Spam buff spells on your party (preferably in combat against something that is unlikely to kill you.) Triggers if there are active buffs, and extends their duration. Unconfirmed, but does NOT seem to apply to automatic buffs like the ones provided by food, only -kaja type spells.
EDIT: It does have the chance to trigger based on skills that provide an automatic -kaja effect at the start of battle (apologies, not in a position to check their names at the moment, but King Frost has one, for example, that ups defense for the first 3 turns of combat.) Your odds are still probably better to specifically spam -kaja spells to try to trigger it, though.

Reboot: This one is slightly more difficult; you need to get into a fight and let folks die. The fastest way I found to do this was picking fights with Rangdas while everyone equipped with Demons weak against Physical, then using Physical attacks against the Rangda, which reflect and kill the party. While Arrow, Saizo and Milady are doing that, Ringo defends and heals herself. The trigger is having at least 2 party members down at the start of your turn; gives a chance to resurrect the party at full health.

Ailment Purge: This seems to be the biggest hurdle for most folks, and I was beating my head against a wall for quite a while before I got it. This one can trigger if at least 2 members of the party are suffering from status ailments, and removes those ailments. You can certainly try doing this against almost anything that can cause an ailment, but fighting with the RNG to have the enemy use the desired skill, for the skill to actually affect the party member, for them to stay affected long enough for a second or third member to get hit too, and for the Command Skill to trigger is hair-pullingly frustrating. What I found, however, is there is an enemy who loves to come in packs and also spam ailment inducing, party wide attacks: Succubus, found in Arrow’s Special Sector of the Soul Matrix. Equip Arrow, Milady and Saizo with demons weak to Ruin, select Succubus as your Search Target in the Enemy menu, and go hunting. When you find one, DON’T slash it (the bonus attack or resulting Sabbath might kill the Succubi). Have Ringo defend, while the others either use buffs, healing items, or cast Ice spells (those heal the Succubi) to waste their turns. If you Guard with the others, it reduces the chances of the status effect working on them. The Succubi will typically start spamming High Pressure, which causes Dread; it only took 7 turns for the skill to trigger.

Once you’ve done them all, the trophy will unlock. I do not know if which ones you’ve used carry over to NG+, but just to be safe I would recommend sitting down near the end of the game and doing all of them one after the other, to make sure you got all of them in the same playthrough. Hope this helped.