We were the only people in the FP line as it was quite late (a late EMH) so the only people who were waved past us were standby people. In fact, he finally let us go when other people came in behind us.
Was this an EMH where they were not issuing Fastpasses, and the Fastpass was for a regular hours time? A lot of times they do not issue Fastpasses during evening EMH, and Fastpass line may not technically be open any longer...
We use the FP's after the initial window has "expired". I agree for the most part that it doesn't make a difference to the total wait times of all guests, especially on busy days when the standby queue never empties. However, there are other dynamics involved, espececially if guests are deciding on whether to ride an attraction multiple times.
That's why I include various caveats in my analysis
One problem that I see is that many guests will enter a standby line based on the estimated wait time posted at the ride and may skip the ride if the posted time is too high. The standby line may not be any longer (same # of people) later in the day, but it may move much slower. WDW may not be able to predict the mass influx of FP's in time to warn the standby riders and the actual wait time can go up much higher than the predicted time.
I expect that Disney actually has a LOT of data about how fast the lines move at different parts of the day on different crowd levels. There are probably not many more people using their Fastpasses late today than there were this time last year compared to the whole. But Disney can change their policies whenever they feel like it if it became an issue.
This seemed to happen to us in the Splash Mountain standby line (40-minute wait estimate) about an hour before the nighttime parade; the standby time ended up being 80 minutes... Normally I don't wait 40 minutes for a ride, but we wanted to make this our final ride and leave to pack our bags. We had FP's for SM which came into effect while we were in the standby line, so we skipped over to the FP line (not our usual mode of operation for efficient use of park time).
Having the standby wait time be nowhere near reality is not unusual, and rarely has anything to do with the Fastpass line.
First, the standby time is measured by those red cards they occasionally give out to guests entering the line. They are read by a proximity reader at the front, the CM hands them to the guest, and then the guest carries it to another CM at the other end, who scans it again. The time is recorded and the updated on the clock. I don't know if they do some funky math with those times, but I suspect it simply updates to be the time it took that card to get through the line, rounded to the next 5-10 minutes. So, says it says the wait time is 30 minutes, and I get a card as I enter, and I get through the line in 40 minutes and hand in the card, the clock is updated to 40 minutes - how long it took ME to get through the line. But a large group of 100 Bohemian Football Pep Squad Gymnasts got in line behind me. Is the guest after them going to have a 40 minute wait?
Second, maintenance issues. Especially at Splash Mountain. It shut down no less than three times while we were there - once while we walking by, and then twice while in line, and we didn't get to ride that day. But it went from a near walk-on to 60 minutes.