Fuelly seems to have problem with odo tracking. Although the FAQ said that the first fuel up is not counted when using odo, it apparently is for average mileage. Right now, I have a lower average mileage than my best mileage, which is not mathematically possible. Changing the amount of gas in the first fuel up changes the average mileage, which shouldn't happen.
Are you just doing total miles tracked / total gallons consumed? If so that's the discrepancy you're seeing. Total gallons consumed and total price still uses the data from the first fill-up. It's just the average MPG that doesn't.
It depends where you are seeing fuelly's average mpg. For my sh150i scooter, I see 78.6 mpg on home page (my garage) and 76.6 on log page. Both claim to be using all 34 fill ups, which includes my first full up. But you know this cant be!
My average mileage is also wrong. The running average is higher than any of my individual fuel-ups. Clearly that's wrong. It's listed at 18.5, but calculated across all fuel-ups (I have less than 10 anyway), the average is actually 15.6.
Luckily there weren't too many fuel-ups to go through, but I edited each one and "updated" them - some required me to re-enter the trip miles - and when I completed the last one, the running average corrected itself to 15.6.
I had the same issue with the average MPG being higher than even my best MPG fill. After doing a fake update of each value, the average corrected itself. Clearly Fuelly has some kind of bug present in their average calculation. I emailed them about this, but got the same response that I can read under the faq.