There are complications when two identical items with different SkinIDs are exchanged.

Let's take Scrap as an example to explain it simply.
I want to buy normal scrap for scrap with skinid. Then the normal scrap is deducted but the scrap with skinid is not spent.

Is it possible that the vending machine accepts the purchases regardless of the skin id?
Then you could trade talers (note with skinid) for coins (note with another skin id)

If you have configured an item to cost skinned scrap (scrap being just an example), then only skinned scrap will be accepted as payment. If you are seeing otherwise (i.e., unskinned scrap is accepted as payment), there must be another plugin interfering, or an issue with the modding platform (Carbon maybe).