I cloned the main site on a multisite and tested a purchase with paypal sandbox

I have a multisite with main and 1 clone of main sub site.
I was testing an order on the subsite. When the order ended up on the main site I looked at the links on the cloned site for the store and the subsite had links back to the original main site not to the subsite. All the other menu items have the correct subsite links.

Is this a bug in wpmudev clone plugin?

thank you