The other day I noticed on the 5 minute MPD FE display a couple of bars at around 90 mpg. I expect that I had been gliding enough to hit 99.9, but didn't think any further about it. Yesterday, I filled up, and for first two miles drove almost all EV. Consumption showed 99.9 as expected, but again the bars over two minutes were less than 99.9. Since the FE had reset after fueling, it was clear I think that a display anomaly is present. I have since seen bars at 99.9, so it is transient, and I do not think affects the very accurate FE calculation Prius performs. Just a curiosity.
Not enough data, expect calculation oddities. The 5-minute bars reset immediately, but you may go a few tenths of a mile before the average resets, so they may disagree after only two miles. Two miles is so little gas that I wouldn't expect any accuracy or even consistency. Wait at least 20 miles before you read anything into the display.
You don't say where you're from... Did the cabin require heat? If so the fuel used in heating the cabin will be factored in, even though you were in EV mode.
The "display discrepancy" may be that the Energy screen, or the instantaneous use bar on the Consumption screen, didn't show that your ICE was really running. Even if you're not heating the cabin, as Brian suggests, the ICE and catalytic converter have to be hot to minimize emissions. It's easy to forget that Toyota designed the Prius to be a low emissions car, and part of low emissions is using gas very frugally. Great MPG is a by-product of a highly efficient power system. I suspect that your ICE was running, so your cumulative MPG couldn't be 99.9. I know my car will sometimes run the ICE even going down hill and regeratively braking if the ICE/cat isn't hot. Like KTPhil said, average over time.
The engine doesn't run to heat the cabin if you're in EV mode. And outside of EV mode, even if it's running without showing arrows, then the instantaneous fuel consumption readout reflects it.
So far, if I've been in nearly pure EV mode, my bars show it all the way to the top, at 99.9. I haven't noticed anything like what you've said, but I'll keep a closer eye on it. I usually do this once a day for a while.
So I got a chance to check my graph response. Ran into some serious congestion on my commute. The graphs were all the way up to 99.9, so none of the anomally you noticed. Here is a pic of my Consumption graph. You can see the first 5 minutes is the initial warm-up period. Then there are two bars of normal highway driving, then comes the traffic, and three bars of EV.