The thing I can't work out is the disappearance of the balls before the refs would normally take them out. The Head Ref (Walt Anderson) said he had never seen them disappear early before. If the Patriots regularly did this, you would have had more reports of that because you can bet they asked around.
So disappearing into that closet looks suspicious. But it also doesn't make sense that it was the first time.
I almost want to say they were tampering to get a 12.5 reading after ref inspection, but this wasn't when they did it. This was just a weird deal. I would bet they were leaking air on the sidelines.