PS - Personally I think rolling extra fees into the postage for "gas and packing material" is underhanded and it really irritates me when I see sellers use this as an excuse for overcharging.
I actually do not see the harm in adding a little onto the postage cost for supplies. It's called "shipping and handling" and almost all retailers do it. As long as it's not exorbitant it's fine. When I sell on etsy I round my shipping prices up because I buy shipping supplies in large quantities specifically for that purpose, so it legitimately is part of the cost of me shipping an item.
I agree with NoDivision. I usually round my shipping charges up a bit to cover the cost of materials. Bubble wrap is expensive, and so are bubble mailers. Plus, there's packing tape, printer ink, gas, time spent waiting in line at the post office, etc.
When I sell on ebay, I always charge a flat rate. Sometimes shipping ends up being a bit more than it costs me, and sometimes it ends up being a bit less. It sort of rounds itself out. Overcharging by a large amount is not right, of course.
I would recommend asking for clarification from your seller, because I really don't believe it cost only $1.25 to ship two baby ponies. The absolute cheapest that first class can be is $2.07 (and that's for a one ounce package), so it sounds like the $1.25 was an extra amount she had to pay for some reason.