Nala, I hope it's incompetence as well. And though I'm not one to suspect Disney of hatching a nefarious plot every time they make a mistake, this one makes me skeptical.
1. I hope we find out that the computer system is assessing that fee IMMEDIATELY upon a reservation time expiring...not because it makes a lick of sense to charge a customer FORTY DOLLARS for being a minute late, but because that at least is a mistake a rookie software engineer might make. If it's programmed for 5 minutes, we can do nothing but assume that it was deliberate.
2. This "glitch" could be solved one of two ways - either by extending the fee assessment time to 20 or 30 minutes after the actual reservation time or by automatically reversing the charge once the guests check in. Unless Disney has the worst development environment on the planet or they've hired completely incompetent programmers, this kind of fix should be fairly straight-forward.
And it makes me think that unfortunately, Disney is in no hurry to fix the issue.
3. The proper way for Disney to handle this would be to reverse the charges for all guests that actually checked in. Because if they don't then they will have knowingly charged some guests both the fee AND for their meal. This is unpalatable to me.