See this also:
In Bright Forest explore, gnome is unable to replace Doom , at least twice or trice for me. 3 rewards only.
@YourMom this is a separate Known Issue, in regards to Doom Troops in Explore battles. Which has been reported.
@Julli-of-North apologies for the delay, we checked your account data for this battle and have since sent through the missing Pet Food from the Pet gnome in this battle. But the Pet Rescue was not missed. I have since sent through your report to the team as well!
Jeto - Support Team Human 
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Im ok with missing few pet foods, but the bug is alot more common than only this on occurrence. I would say i miss reward from maybe every 5th to 10th battle in pvp. I do suspect it has got something to do with the immunity on hero. If you see the link, there was battle with Ironhawk that has Impervious trait.
I suspect all these bugs are related to that they still not implemented a separate troop killing/replacing/removing mechanism but they are reusing an existing mechanism.
Dooms are invulnerable so that must prevent the gnomes to kill them.
Similar issue was with lycanthropy which originally used devour, then death mark, none worked perfectly.
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Just updating this. The bug seems to be still alive.
Here is a recent screenshot from pvp i did.
And this is his team taken from battle log.
I suspect the culprit is King Silenus with his Impervious. The gnomes arent just working correctly and this means lost rewards for the players. Im pretty sure King Silenus would have dropped a second epic vault key 
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Hero still not get replaced by GAP