I went to run the Mini Challenge and found that it also included other cars instead of all Minis. I did choose Mini Challenge from the selection and not ALL. Another example is I have the Renault Clio Cup mod installed but it appears with Opala Stock car 1986 mod.
Is there a way i can tidy up the game to just get the correct championship cars to show up in individual championships.
What you want is to have a specific rfm like Patrick mentioned but also the corresponding vehicle class number.
For example, for the ClioCUP mod:
Change the ClioCUP .rfm filename to "reiza220.rfm" (I picked 220).
Inside that rfm, change "Vehicle Filter = OR: Reiza20" to "Vehicle Filter = OR: Reiza220"
Now go to the ClioCUP vehicle folder where the .veh files are located. Mine is <SCE_main_folder>\GameData\Vehicles\CLIO CUP 2013\RD Clio Cup. Then, in each VEH car file, change "Classes="Reiza20..." to "Classes="Reiza220...".
What happens here is that Reiza picked class 20 for their Opala86 cars. Thus both the Clios and the Opala86s have the same class ID and ends up in the same car list.
I think step 1 is optional here but it helps keep things tidy.
PS: it works the same way for any car mod and it helps you avoid any "car filter conflict".
---EDIT---
"What happens here is that Reiza picked class 20 for their Opala86 cars."
This was true in ealier versions. Since 1.50, Reiza's changed their class IDs and there should be no conflict between the ClioCUP mod and Opala's (as far as I can understand it). Opala's RFM is reiza02.rfm. You can check it in there.