I finally solved this mystery, so here is the answer for anyone else who has this problem.

My MIDI keyboard for some nonsensical reason outputs on multiple channels at once. This causes duplicate notes to be sent to HISE which causes the group counter to increase twice for each key press. So the solution is to filter the incoming MIDI channel in HISE preferences.

@d-healey said in [bug] Pasting samples into group not working:

In the sample mapping window, no matter which group I have selected pasted samples always go to group 1.

If you copy/paste your samples, they are indeed pasted in the 1st group but after pasting them, if you immediately click on the RRgroup + or - buttons at the bottom of the sample map, it moves the samples to the desired group. Even if they are not selected you can still move them...
(Hoping you don't have too many groups...)

Edit : tested on macOS, commit from Jul 25 :)