The boxes are all sorts of screwed up. I don't know what happened, but I would expect that they will look at it and fix it for the next set.
I'll use my stats for the 24 boxes I opened up just as a reference point.
I pulled 10 Shiny Pokemon. I didn't pull a FA in ANY box I pulled a Shiny.
I pulled 3 NON-FA Ex in 2 boxes
I pulled 1 NON-FA Ex in 4 boxes
I pulled 2 NON-FA Ex in 18 boxes
I pulled 2 FA Ex in 10 boxes
I pulled 1 FA Ex in 1 box
I pulled 0 FA Ex in 13 boxes
That's not even getting into the RHs which have some funky distributions. I pulled 22 RH Bidoof in 24 boxes, and only pulled 2 full RH sets. The set was strange. It was like someone decided to mess around with the Ratios. I hope they fix this for the next set, cause it's annoying to have such hit and miss boxes, especially if you only buy 1 or 2 boxes.
If there are 6 Ex and 6 FA in the set, you should get 2/1 on them, with a chance of 2/1/1 with the Shiny. If there are 8 FA (which might be the case in a few sets), it should be 2/2/1 with one of those FA being one of the two trainers.
Drew