solved, I just did not use the shops in the end, this way the items don't get duplicated.
Not sure why but it's showing duplicate of all items on each npc. The strange thing is that in my localhost is normal, but in the host server is duplicating all items, one normal and one item with discount price (for all characters classes).
I found out that loading the npc manually by using @loadnpc the items being sold in the shops do not get duplicated, but if I set the script to be loaded using script_custom.conf all the items on those shops get duplicated. In the map-server I get warnings saying that the items are being sold for free (but they are not since it's a quest shop), and if I set the price to 10 or some small amount it says Item xxx [IDhere] discounted buying price (1->0) is less than overcharged selling price (5->6) in file 'npc/custom/quests/quest_shop.txt'
Is there an easy way to solve this or I will have to make Emistry Patch to disable discount on that map and items?