You should submit the bugs here https://www.advancedcustomfields.com/contact/
The only suggestion I can make for bug 1 is to use unique names for your field groups.
As far as bug 2 goes, if you are including the same field group multiple times in the same clone field then this is not a but. The fields will get the same prefixes and end up having the same field names and keys. You would need to use different clone fields to include clone the same group multiple times.
