That sounds like some fraudulence to me.
The reason it randomly crosses up is because it was just a poorly designed move. The reason it crosses up is because sometimes his flight path will miss the opposing character just long enough that they come out of blockstun, then he'll travel behind the character and end up hitting them from behind. Generally speaking, if you're in the corner when someone throws out Phantom Dance, you're completely safe. Mid-screen, it's fair game(pushblocking increases your chances of being hit, just as an fyi). Otherwise, hope luck is on your side.
Case in point.
The only way to fix it is if they increase blockstun(which would be bad), or make it travel a set path, which, depending on how they do it, could end up being a buff or a nerf. I honestly don't expect them to change it, though.