For import order to PrestaShop, we need to know the corresponding product in PrestaShop. 

To find it there two way
1) For items that listed using PrestaBay we have data in DB where to save PrestaShop Product ID <=> Ebay item ID
2) For item that not listed by PrestaBay, we can find item using ebay SKU and PrestaShop Reference

So when new orders happen, PrestaBay insert data about it into Catalog->Ebay->Orders and try to find all products in PrestaShop to import it.
If an item listed by PrestaBay mapping found in DB. If item not listed we look up by Reference.
If PrestaShop product references different from SKU on ebay, you can have PrestaShop order with an invalid price.
For example:
PrestaShop products:
T-shirt A: Reference: U1
T-shirt B: Reference: U2

Ebay items:
T-shirt A: Reference: U2
T-short B: Reference: U1

So when customer purchase "T-shirt A" on ebay, in PrestaShop order will be created for "T-shirt B".

Very often this happens for variation listings. Instead of import order with combination option, imported product without any options (in case of primary product SKU same as purchased ebay item).