I have a Gnomish Merchant (rings) and in the High Mountain Valley store, I can buy certain gems for less than I sell them to the Trollish shopkeeper.

Haggling of 97, 19th level,
two uncursed sapphires cost 926 GP to buy, but I can sell for 1296 GP.

However, dropping one uncursed sapphire, I can sell for 324 gp. (buy for 463 gp)

So it seems there is some glitch in the pricing when dropping multiple gems (or items in general?)

Actually, it's for all stacks of items - for example, necklaces of the silver tongue