Yeah this is as I suspected.
Basically what happens is that with this new patch, clicking the button makes a proper calculation and your pet can jump directly from 3->5 when you apply the points on your dragon.
So to stop this, they made it so pets that are already training at this patch (4->5) are fine.
But it wont let you click button again if you didnt click it prior to patch, as that would risk it jumping to 5->5 directly.
Anyway, they should've been more open about this. I know a lot of people who wanted to leave their pets pristine.
They fixed slot jumping back in Pub98 though, and made it so pets can only increase in control slots once per training cycle. I don't see them reverting that, as it would cause a lot of issues. It would also cause other legacy pets to potentially slot jump again, like WW, Nightmares, Banes, and Dreads, but those seem fine this patch.
I think the "broken state" they are referring to is specific to legacy Dragons. If you train too much into the last level, the Dragon will either revert or lose it's remaining training points. I guess they didn't want anyone else to train Dragons until this is resolved... which would be admirable if it weren't for the fact that it makes absolutely no difference since there are already lots of fully trained legacy dragons to worry about out there, so people training new ones really shouldn't matter...
Unless they are not confident in their ability to correctly catch exploited pets without targeting legacy dragons, and this is a "safety" measure to minimize more potential lost legacy dragons when the revert fix goes live.