4 3 2 1 - 1 2 3 4

So each number has their own turn, 1 - 1 roughly go at the same time with the obvious exception to the rule being initiative, then 2 - 2 go, so on & so fourth.
Both sides take turns in that order regardless of where the ninjas are placed, if you have an interrupt in slot 2, you can never land your interrupt on slot 1 that's just the basics of how the mechanics work. Slot 2 can interrupt slot 2 & below, but if slot 2 uses his mystery exactly on his turn, he will go- regardless of initiative & this goes for all numbers below, slot 2 interrupt can't actually interrupt anyone if they use their mystery on their own turn, a perfect way to replicate this & notice it, is with Mei- on Mei's turn she uses her fog to poison, if you use her mystery precisely during this fog she will proceed to use her Mystery & you can't stop it.

To fix it, you'd have to implement some sort of delay & check factor during the point a mystery is used- so the entire board would stop for a split second allowing time for the game to pick up an enemy interrupt.

I could be wrong, but since starting this game all I've done is Arena because it's like the only thing to do & this is basically what I've noticed.

Yea, that's what I was saying as a potential fix, there should be a delay added into the position before a Mystery right when a mystery is being used, so that if someone decides to use that mystery when their round(attack) is queued, it'll add a "Pause" and then it should give enough time to pick up on wither the enemy has used an interrupt or not.
Now obviously I don't know the ins & outs of the system, this just seems like a logical fix- but it may not be as easy as it appears as we don't know much more than what we can see during a battle.