Nice work on your game! I did struggle to kill the second boss as even though his health reached zero, he didn't seem to die and when I got too close, I died myself. However, I did enjoy playing! :)
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I am not sure if this bug or not. But by listening your words.. It Dosen't sound like a bug.. You might hurt enemies ( frying koopa ) shield bar ( the Grey bar ) instead.. If this is the case.. Then you didn't kill it completely.. You need to destroy the shield first.. And then kill it.. Same goes with other koopa on other side.. And try to stay away from them little bit.. To avoid getting hurt.. If you did exactly that i said.. You should continue play the game perfectly fine.. I don't know if it was obvious or not.. But Regardless.. I hope this helps :)