So, after some testing and asking people here and there, and doing some testing in nexus blitz games myself, I can confirm how the bug plays
You need to have a specific rune page when loading into the game. You need both Ultimate Hunter and Cosmic Insight. Those two runes are what cause the problem. Outside of that the bug reduces the cooldown of Neeko's ultimate, and her summs (except from smite, he gets charges but cant use tham more often than 15 seconds) to 0.
Other than that, I have also noticed that each time she transforms with those runes, she gets the debt cap from Future Market extended, getting to a point in which she can have negative 3k gold
Hope this helps Riot solving the issue by deactivating the specific runes, I wouldnt like to have Neeko yet again disabled, if it was possible to get only those two runes disabled, that would be great