Most people think 'programming' means simply making up workouts. It doesn't. Programming is a systematic and thoughtful arrangement of sessions towards an end result.
I liken it to making a quilt (something I've never done but I understand the process of). Ideally, you have a design for your quilt and then you work backwards. With a design you will know where each square of cloth gets placed and how to interlock them to get the desired effect.
Two things are necessary for this to happen:
1. You have to know what you want the quilt to look like (so in our case, what is the desired outcome of the program).
2. You have to know which squares (training methods and modes) to use and how to assemble them.
It takes an understanding of the physiological effects of training and years of solid strength and conditioning experience to accomplish 1+2 together.
If one or both of those components are lacking, then the programming will suffer, typically resulting in a disjointed day-to-day approach (i.e. we did squats on Monday, so we shouldn't do them on Tuesday!). In these circumstances, who knows what the quilt (or resulting fitness) will look like.
I should mention that for a lot of Crossfitters, this simply doesn't matter. They just want to turn up and crush themselves. However as an affiliate owner or coach you have a responsibility to offer high quality service to your membership (they are paying premium prices after all), and that should involve a thoughtful, reasonable, and effective approach to programming.
Keep fit and have fun,