Xbox series S
Every time it created a skull it kill my troops in one hit it says it does double damage to green troops but I had no green troops.
“It’s not a bug, it’s a feature!” 
The Eagle Eye trait applies Hunter’s Mark to the troop first, then the skull hit happens. So it deals double damage always, as long as the troop being hit is not immune to Hunter’s Mark (eg. Impervious). Plus extra damage when enraged.
Webspinner works similarly, it webs just before it skull hits, then does double damage because the troop being hit is webbed 
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Personally I disagree with the design of “inflict status ailment before calculating skull damage” when said status ailment directly impacts the calculation of that Skull Damage (mostly Eagle Eye, but also Knockout, and a few specific combinations like Webspinner) – I remember hating Harpy Eagle with a passion when I discovered its trait functionally doubled Skull Damage to basically 90% of opponents, and there are ~8 total troops with Eagle Eye as a trait.
But I respect it is FAR from the only passive trait that can cause a troop to deal unexpectedly high amounts of Skull Damage (compare “[Element Color] Hatred”, “[Troop Type] Slayer”, “Godslayer” / “Siegebreaker”, “Razor Armor”, etc), and given how often I run teams with some access to Barrier it’s not too difficult to work around.
And, yes, I’ve intentionally assembled a few teams with Eagle Eye in the lead specifically to enjoy having this behavior work in my favor.
But if we want to discuss the underlying question further, there could be a reasonable argument that these passive traits should take effect after dealing Skull Damage, for two reasons:
1 - If no Skull Damage is actually dealt (due to e.g. Barrier or Entangle) then the passive trait does NOT trigger. (Contrast that similar traits of “inflict [status effect] when I take damage” always trigger even if the damage was negated by Barrier)
2 - There are already a plethora of spells to the general pattern of “Deal damage. If the enemy has [status effect] then cause [extra effect]. Next, inflict [status effect]” (e.g. Captain Macaw) that would be obviously OP if their order of effects were reversed.
And if you want to argue that both effects should take place “simultaneously”, the only logical interpretation of “simultaneous” I can think of is that each effect must be processed in ignorance of another. i.e. the game saves a copy of the troop’s prior status and calculates all effects based on that copy, then combines the results.
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You are absolutely right, just the devs do not care so we will have to live with abominations like these.
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