Incorrect costs of goods calculated when 2 or more batches are received thereby throwing out financial records and quoting ability

When i make a PO and the received stock comes in with multiple batch numbers and Best before dates i need to use FIFO batch as an ordering method. This is also essential if there is a issue with a particular batch and a stock recall is required.

When stock arrives and I receive it into the system, i have to convert it to an advanced PO so that i can record the batch numbers and best before dates. During this conversion process and disassembly process, It does not calculate the costs of goods correctly and thus throws out my profit and loss calculations for every product that i use these ingredients for, which essentially makes this information useless. I cant see why the same ingredient on a PO gets 2 different costs of goods when the costs is the same. To suggest that this is not a programming issue is very strange. I need this rectified asap.