As I stated, contract will always use time dependent condition, you can't use time dependent condition for contract (and info record), for more details read the OSS note 456691 - FAQ: Price determination in purchasing question no 2.
I assume, there are nothing about custom pricing procedure in your case, you are just using supplement conditions in contract and it is flowing in PO line item condition.
Whatever you are facing it is the standard behavior. System will pick both condition types which is maintained in Contract - supplement condition and which is maintain in calculation schema (with combination of purchase organization and vendor).