When buying 1 of something from a vending machine, say at the Outpost, you get two if you have enough scrap. For example, if I have 100 scrap on me and I want to buy 1 item that costs 50 scrap, it will take 100 scrap and give me 2. I confirmed this by unloading the plugin and trying it and the vending gave me the correct amount.

For vending machines where you can reproduce this issue, have you customzed them with Custom Vending Setup (CVS)? If so, it might be a conflict because both plugins use the same hook to override the behavior of transactions. This is new behavior for CVS since folks such as yourself were asking to be able to skin currency. To determine whether this is the case, you could try buying from a vending machine that has not been customized by CVS, since CVS shouldn't affect the behavior in those cases.

Yes, I do use that and I've been told by my players that this has been happening for "a long time" but they didn't give me a solid time frame. All of my outpost vending machines have been customized. 

I submitted a patch to Vending Manager to fix the double transaction processing. It works by making Vending Manager ignore transactions for vending machines customized by Custom Vending Setup. Hopefully the patch gets merged soon. If not, you can message me on Discord to ask for it.