If the Coke was coming out clear, that's not the fault of RapidFill. That's the fault of the cast member for not changing the BIBs in a timely fashion. It's like blaming your car that you ran out of gas.
Better analogy might be blaming the car for a skid because the rental company provided it to you with balled tires.
Your analogy says "your" car which implies it is the driver's/user's fault and obviously, that they apparently ignored the warning lights on the dash. In the case of a soda machine not dispensing soda properly, unless it warns you that the syrup is out or prevents you from trying to dispense the soda, it's the fault of the operator. (BTW, freestyle machines actually do prevent you from selecting flavors not currently available)
While the fact that the machine has effectively blocked you after not dispensing your product may not directly be the fault of the RDIF system, you can't really argue that this is a problem that would have existed without this system because without it, the consumer could do what they do every time this happens anywhere else - pick another option.
Whether it's the fault of the technology or the maintenance on the equipment that the technology assumes will work perfectly is kind of moot as this was a problem created by the operator that potentially burdens the customer while providing no benefit to the customer in the process. The operator determined that the minor degree of complexity and annoyance for typical customers and the failure of the system for a select few - an overall loss in consumer experience due to an "advancement" on an appliance that has otherwise faced few issues for roughly the last century of its existence - was acceptable.
I know at Universal, they have a simple fix for this when their rapid fill cups aren't working with the freestyle machines (which actually do provide an enhanced experience for the customers using them in the park over what their options were, previously). Employees have credit-card sized pieces of plastic with chips in them that "unlock" the machine for fills. They just put the card down, you put your cup over it and it works.
Kind of surprised Disney doesn't have a quick and simple solution for situations like this, too.
Then again, maybe they do and this particular cast member, not usually assigned to food, was not aware of it?