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The cloning-phoenix bug is not really squished yet. I've attached a saved SP game where my Phoenix gets trampled by some elephants, and gets cloned on rebirth from Phoenix Pyre (his first clone is at the top of the battleground screen):

...
damage 19 on Phoenix, spec0x200000 ba0
blastsqr: unr1348 x21 y16 aoe50 dmg10 eff2 spc64 as10133 al9
...

The independents kill him after he clones:

...
Immortal/Twiceborn Phoenix perished
immortal resurected
looseallitems: cnr 99(Teh Bird) unr 1348
...

But the clone does not die, it spawns a new unit even though the original Phoenix died, the fight goes on, and the indies ignore both the clone and the cloned clone:

...
gettarget player 25 targtype 5 unr 1129 eu -1 mode 0
Get an order for 1130 Heavy Infantry, ord 0
Closest enemy (for unr 1130)
...

So, the battle goes to turn 70 with everyone just standing around, and then the indies rout:

...
----- turn 71 (rand 628)(check 17051815)
Battle running along just as I have forseen
battle_incheck
rightplayer teamhp 598 max 713
Army rout 100 for Independents
Mrlreport (right): good40 broken1 autobreak130 turn71
autobreak 130 for Independents
...

My cloned Phoenix has permanent 115 fatigue, so it can't flee even though it wants too:

...
leftplayer teamhp 0 max 17
Army rout 100 for Marverni
Mrlreport (left): good0 broken8 autobreak140 turn71
autobreak 140 for Marverni
...
----- turn 78 (rand 401)(check 2516329)
battle_incheck
rightplayer teamhp 0 max 713
Army rout 100 for Independents
Mrlreport (right): good0 broken22 autobreak130 turn78
autobreak 130 for Independents
broken unit 1124 removed from bg
broken unit 1136 removed from bg
battle_incheck
_____The winner is 3_______
leftplayer teamhp 0 max 17
Army rout 100 for Marverni
Mrlreport (left): good0 broken22 autobreak140 turn78
autobreak 140 for Marverni
...

Turn 78? That's unusual. Anyway, wierdness all around.