The two main reasons this would most likely happen are:

1 - Domain is not added to the white list of domains in CFProTools - double check to ensure you've added both your live domain and your CF sub domain to the whitelist in the DOMAINS Tab in CFProTools.

2 - Product ID's are not paired up correctly in the PayPal Plus configuration in CFProTools  -  for that, just double check the product ID's are correct for the Stripe/PayPal pairing.   If the PayPal one is wrong, both product variations will show up in the core products.