I never questioned it but now that you say it... ur right I don't understand either. But maybe its because after she did like her own world for Enzo (idk how its called) she maybe became like really powerful and her Grams and the other Witches had been the motivation but idk... good question

If you pay attention to Bonnie’s magic at the end of season 8, her magic had grown to the point that she had become powerful enough contain Hellfire all by herself, controlling it over 8miles without looking, and held it off again. In the past, it took 100 witches magic to pull off that feat. And she did it by herself. Then, by drawing power from the Bennett bloodline (not coven), she destroyed Hell. Hell was a world-wide dimension and she was powerful enough to destroy it, freeing millions of souls all over the world.

The reason I brought this to mind is to draw attention to Bonnie’s power growth. At this point, she might have as well been one of the most powerful witches in history because she performed feats that no other witch had performed and did something that affected the entire world with her innate power but also drawing from a nigh-inexhaustible source of magic. So, obviously she’d be more than powerful to break a spell said to be “unbreakable”, given that she would have become much stronger than the Gemini coven leader, Kai (Bonnie even showed signs of being more powerful or equal to Kai’s magic in season 6).

Kai would have used magic to rig the spell to be that way and used magic to close all the loopholes because it is usually impossible for a spell not to have a loophole. Impossible. So if all the spell’s loopholes were removed then it must have been magic making that possible and Bonnie’s magic simply became greater than that and trumped it.

Either that, or she simply became smarter than the Gemini coven leader and found a loophole despite Kai’s claim. That or Kai simply lied about the spell being unbreakable and without loopholes because he wanted to scare them from trying.

To break a spell said to be unbreakable/indestructible you have to either be more powerful than the caster or smarter or both. Either way, Bonnie would have had to surpass either Kai’s power (which she already has) or his brain or both to break the unbreakable spell. This would mean her understanding of magic grew to a point that she was able to break the spell’s waterproof clause.

I would think that she worked her way around the spell just like Josie change the rules to Professer Vardemus' box

Writers and their inability to keep track of their established Lore. Bonnie dying, momentarily, then coming back should have been all the explanation needed