Check engine light and HUGE discrepancy between computer and gas gauge mpg – any ideas?

1) Dealer 'fill' may have just been enough to light the top pip, rather than truly full. If so, your top pip would have gone away quickly. Fill the same way each time: I'm a 1st click=done type, but others go to 2nd or 3rd shutoff, still others fill until the neck is full. I sacrifice tank by tank accuracy using 1st click, but no risk of spillage or damage to emission systems.
2) When you get to the last pip, you still have some range left, although you should fill up sooner than later as discussed here many times due to the bladder in the 04-09 models.
3) Maybe a prankster friend or a thief got to you with a siphon hose.
4) Maybe there is a fuel leak.
5) You didn't state how many pips are left, just nearly empty, so we don't know what nearly empty means.

Suggest you fill up now and record your miles in the new tank by pip (some go quicker than others) so you establish a base line and learn the car's gauge.

I'm sure things are fine, but you'll want to calculate mpg manually to compare with the car's estimate, keeping in mind that this 1st tank is probably off due to 1 or more of the above, or other factors.

 

I agree with Stathead's assessment of your mileage issue. I suspect it wasn't actually full when you drove it off the lot. Like any fuel gauge, the Prius' gauge does not map linearly. I've gone anywhere from 50 to 300 miles on the first pip, with considerably less on the rest. Don't fret about it until after you've established the baseline he suggests and find a consistent trend.

The CEL is almost certainly an unrelated issue and would be of greater concern to me. There is no way of knowing what it indicates without knowing whether the car is running properly (though I'll assume it is since you didn't report otherwise), and it probably will require the dealer to pull the diagnostic trouble code(s).

 

I believe that (amongst other things) not properly tightening your gas cap can sometimes trigger a check engine light. Reseat the gas cap taking care to make three or four full revolutions with it to be sure it's sealed properly. If that's it, the light should go away after a few trips of 10 miles or more (it doesn't go away immediately). But, since you just bought it, see if the dealer will check the code for free...

 

Or find someone with a scangauge or other scantool in your area... I completely missed the CEL issue in your 1st post.

Glad to hear your didn't even have the top pip when you got the car and still had 2 left. I think you are getting roughly the fuel economy the car is reporting. The middle pips can go quickly.

 

AAMCO & some/most? auto parts store will pull a code for free. This is why you should buy a ScanGauge if you don't want the extra instrumentation. My bet is loose gas cap. Sounds like the dealer will do this for free under warranty but you'll waste much more time there.

 

As for the CEL, make sure the gas cap is on tight. If found loose, it will take several start/shutdown cycles for the CEL to clear.