With respect, I think everyone is kinda missing the big picture. WSB doesn't have the market cornered on so called "box squats". There are many uses for the box. It would be more accurate to say that neither you nor the football players you saw are doing a WSB box squat. And I do admit to know nothing about what the football players were doing although to me it may have been a modified jump squat - however, the lifting of the feet and thereby placing the entire load on the spine may not be the wisest thing to do depending on the load. That aside though....Sounds like you are using the box as a means to manage squat depth; there is nothing wrong with this and it is not necessarily wrong. You could use other tools to accomplish this but it doesn't make it wrong.
The WSB methodology is intended to break the stretch reflex by briefly sitting/pausing on the box, relaxing the hips and then exploding back up; it is intended to build explosive strength. A secondary benefit of the box, for the powerlifting especially, is that you are always ensured of hitting depth. In addition, a box teaches you to "sit back" into the squat which is the desired means, for some, of squatting powerlifting style. Other styles include sitting down and opening the hips/knees ala olympic style. But WSB doesn't always use a "legal squat" depth box. Variations include a very low box, high boxes and everything in between.
I guess I'm trying to say you need to know what you are trying to accomplish before you decide if something is "right" or "wrong" as there are acceptable variations on the box squat theme.
What are you trying to accomplish with your girls?