"She can't negate or remove the seals placed on her by Kumogawa"

It's literally said by Kumagawa that the only reason the seals are still there is because Ajimu herself wanted them to be held, Ajimu wanted and let Kumagawa seal her, as said by Kumagawa himself. She didn't remove the seals because she didn't want to.

"She can't negate the irreversible destruction caused by Iihiko."

IIhiko is an odd case, the reason Ajimu cannot beat or affect him is because she feels bound to the Theory of Narrative Causality, so for her she cannot beat the "Hero/Main Protagonist" (Medaka and Iihiko) not because of power, but because the Author himself says so. Like how Medaka herself says she would be utterly stomped by Ajimu, but Ajimu says she can't beat Medaka simply because Medaka is the "Hero".

And remember, as shown several times after she was "killed" by Iihiko, she didn't really die at all, she shows multiple times, albeit not physically. And also remember that as stated by her letter at the end of the series, everything that happened was literally nothing more than just "playing" for her, even the Iihko situation, which makes it even more debatable if the Theory of Narrative Causality is even a thing or just her limiting herself.

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