I just deleted out the miles that I didn't have any data for. It's not ideal, but it'll work I guess. Thanks!

If you're tracking by Trip Miles, simply omit the fuel up you do not have data for.
If you're tracking by Odometer, mark the next fuel up as Missed to indicate there was a missed fuel up prior and thus an unknown amount of miles had been traveled between them. This will essentially start your tracking over with that fuel up (like zeroing out a Trip Meter).

Today I had similar issue.

I had a partial fuel-up.
Previously to adding it to Fuelly, I had a 11.3L/100km average, which is rather correct.

I added a Partial fuel-up for 5 liters, and now my average is 5,7L/100 km, which is way off.

I did select Partial Fuel-Up checkbox.

Mazda 3 (Mazda 3) | Fuelly

Did I do something wrong, or it calculates as expected?
I thought that entering a Partial Fuel-Up won't change the Average L/100Km value until next full fuel-up.

Fuel economy shouldn't have been calculated for that partial fill. But partials still contribute to your overall averages. Did it balance out after you added your full-fill on the 3rd?

Yeah, now the average is 10,5, which is rather correct, I suppose.