Back in the day, I worked in fast food. While part of the problem may be the person looking for the right button to press, part of the problem may be the cashier's natural ability to process a spate of disparate information, especially when it comes to them aurally, rather than in writing. Some people can make a mental list in their head of what they're hearing and then press the buttons in order. But MANY people do not have that natural ability and simply can not do it. They are not stupid or ignorant, their brains do not work like that and no amount of effort can make them acquire that ability.
As a result, when I give an order with non-standard requests, I wait until they have keyed in the basic information, then slowly list what I want. And FTR, when I do so, the cashier invariably asks, "Did you used to work as a cashier?" because they realize someone is talking their language, as it were.
I've never worked as a cashier, but what you describe is what I always figured was going on. Sometimes it's hard to guess what order to present information so that you're giving it in the same order that the cashier needs it.
The other thing that comes into play here, though, is that it's really easy for people to go into auto-pilot when they are focused on something other than what a person is saying to them. I know I have a hard time processing information (especially spoken information) when I'm trying to multi-task, so it doesn't surprise me that cashiers in fast food restaurants seem to have the same problem.
So if you rattle off your whole order right at the beginning while they are trying to input the basic stuff, process what you said, and then remember it in whatever specific order is necessary for the system (or necessary for them to communicate your order correctly), chances are good they will have to clarify what you want and that they may get something wrong. That's especially true if your order is anything outside of the ordinary.
For example, I pretty much always order Diet Dr Pepper when I can. I don't like Diet Coke as much, and I don't drink regular soda at all, but it's far more common for people to order either Diet Coke or regular Dr Pepper. If the restaurant is really busy (or if I'm going through a busy drive-thru), I will say I want Diet Dr Pepper right at the beginning of my order because it seems to help make sure they don't hear me wrong. But I always expect to repeat myself when I do it that way.
It's generally much more effective if I can say that I want a number 5, no pickles, and then wait for them to ask me follow up questions about what drink I want, whether it's for here or to go, and what size meal I want.