That's pretty common for flavorings... the difference in price per ml goes way down when you buy bigger bottles. There are a couple of reasons for it: it's more work to make a bunch of little bottles, and people at first will buy a ton of little bottles to sample different flavors to see what they like. If 80% of my flavoring sales are 3ml bottles, that's what is going to be a little more pricey... supply and demand. Most flavor vendors price the same way... TPA offers 4ml bottles for $1.40, while a 1oz bottle (just over 30ml) is $5.50 depending on the flavor. What you are seeing is totally normal.
Thanks for the info.