Yes, 'by' in these examples refers to the amount of the change in examples 1 and 3, and the amount the person was overcharged BY in example 2.
The price of oil fell by a further $2 a barrel:
1) Let's say the price of oil, which was falling over some period of time, was $10 a barrel at some specific point in time. At a later point in time, after it fell BY $2, and therefore the new price would be $8 a barrel.
I was overcharged by £3
2) In the second example, where overcharged means the person paid too much, the amount they paid was £3 more than the normal price. Let's say you bought lunch at a restaurant and the normal price was £10, but for some reason the waiter charged you £13, we can say you were overcharged BY £3.
They are expected to increase by 10% this year in China
3) Although the third example uses a percentage, the idea is the same. Let's say the price of a what's-it in China is 100 RMB, but the price is expected to increase BY 10%. In this case the future price of a what's-it is expected to be 110 RMB, as 10 is 10% of 100, and the number BY which the price increased.
Compare these examples if we change the preposition from BY to TO in examples 1 and 3. In this case, the number after to is the value AFTER the increase or decrease, not the number OF the increase or decrease.
1)Oil was $10 a a barrel, and then it decreased so the price was $2 per barrel. In this case we say the price dropped TO $2 per barrel. Another way to say this would be: Oil dropped BY 8 dollars per barrel, meaning the difference between the starting price ($10) and the final price ($2) is $8.
2) In example 3, let's say banks pay 5% interest, and for some reason this changes, and banks will start paying 10% interest in the future. Here we say the interest will increase TO 10%
Another way of saying this would be interest will increase BY 5 percentage points (but not 5%, which would only be an increase TO 5.25%, because 5% of 5% is 0.25%)
Hope that helps!