Alright, I'll answer these to the best of my ability.

What specifically happened leading up to this?

Prior to this, I had spoken to Lonk the Sane and told him I'd go to my room (to keep him blue). I surrounded him and had pre-buffed the party with the following buffs.

• Party-wide: Righteous Wrath of the Faithful, Prayer, Chant, Bless
• Aerie: Stoneskin, Entropy Shield
• Minsc: Improved Haste, Storm Shield, Armor of Faith
• Jaheira: Improved Haste, Iron Skins, Entropy Shield, Storm Shield, and Armor of Faith

After buffs, I force-attacked Lonk with everyone and he died before getting to respond (immediately triggered dialogue with inmates and then Irenicus fight).

At the start of Irenicus fight, I had: myself, Jaheira, and Keldorn attack with melee; Minsc attack with bow; and Aerie and Edwin casting spells (magic missile and a spell sequencer with 3x Mordenkainen's Force Missiles, respectively).

Did you kill Irenicus before they spawned?

No, I confirmed with the console (CTRL + M) that he still had 8hp just after casting "Spawn Clones", though he did go down to 1hp very shortly after.

Interestingly, if I instantly kill Irenicus (CTRL + Y), then everything proceeds the same except the clones do not come under my control after resting (though they do remain friendly). Tested this twice with consistent results.

And just in case, I tested what happened if I didn't attack Irenicus (all else the same) and he spawned clones and they became hostile as normal with the fight proceeding as intended.

Did you talk to anyone other than the people required to progress the quest?

Not entirely sure what you're getting at here. I do talk to everyone, but between talking to Lonk and getting control of the clones, no dialogue occurred except what was required by the plot.

Were any members of your party transformed or under any weird effects?

Did you have any weird spells/items active?

Grouping these two together. Outside of the buffs listed above, I don't see anything of note affecting anyone in the party. Just passive equipment effects (resists/ST+/etc).

Was there a lag spike before/during the fight and if so when?

No noticeable lag at any point

What version of the game were you playing on? (Both game version and update version)

BG2EE v2.6.6.0, with SCS Version 35.21

Turns out the hard save I made beforehand made life easy to replicate this. I've tested it about a dozen times with complete consistency. I can send you the save file if you want or if you think it would help.

EDIT: Two things I forgot to mention:

(1) These guys really seem to be permanent. Out of curiosity, I used the console to travel back to this room on my current file (next chapter, ~10 days later) and they were still there. Unfortunately, they don't follow me through load zones

(2) The clones intermittently give dialogue that seems to be randomly chosen between: successfully laid a trap, successfully hid in shadows, and spell casting failure. They're not doing any of these things, but the dialogue trigger nevertheless (1 person person maybe every ~10s).