Just happened to me as well.

Had this happen to me as well. Luckily I won the match afterwards, but it still cost me 2 creatures that weren't supposed to die and could have cost me the game.

Happened to me aswell. See comment of TorbSean for more clarification aswell.
I attached my logfile, fyi.
Happened in a Sealed game match and lost me the match... wish I'd get back a token for that :-/

Experienced this same bug.

This happened to me. You can clearly see how much energy I paid in the screenshot. Wrath of the Skies wiped the board including the 3-drop when I paid 1 energy

As @Rezzagan#77802 misunderstood what I meant, I will try to clarify. Apologies for the confusion.

I cast Amped Raptor, gain 2 energy. I exile cards from the top until I exile wrath of the skies. I decide to cast wrath of the skies.
I choose the cost of x = 0, paying 2 energy to do so, as Amped Raptor requires.
Then, Wrath of the Skies resolves.
I choose to pay 0 energy, which should destroy all relevant permanents with mana value 0.
However, it destroys permanents with mana value 2 or less, mistakenly including the energy paid through the raptor's ability.

Hopefully this clarified what I meant!

No bug. Raptor gives you energy, then you get Wrath of the Skies, which gives X energy and then lets you pay any amount of energy (up to all you have at that moment). Then destruction happens based on how much energy you paid. No mention of any energy specifically gained from Wrath. Any energy can be paid. This is how all those energy cards work and have always worked, you can overpay with more energy than what the card gives you, if you have more energy to spend.