If you remove more than one ninja from formation, then put them back in, this will happen.
But if you replace ninja on formation with another ninja, the equipment will stay with the replacement (thus when you replace it back, it will return back to where it was)

I think it is because the game has equipment assigned to ninjas, and when you take ninjas off and re-add them, it doesn't remember where they were so it just throws them on where they want to.

there should be a way to atleast lock the equipment you need in a certain ninja. like for example if you need to do sa's or get your nine tails team out or even gnw teams its gonna be a pain to keep switching the ninja equipment to get your magatamas and intitiatves and such on that one person

Hey

Personally, I do agree with the selective equipment, or even an equipment page (1.Tanks, 2.DPS) etc.
Thank you for the suggestion.