I have to manually install configuration profiles on our Macs using a package and stumbled upon the JSS trying to do the same thing. It sees a profile there and tries (but fails) to remove it.. over and over again.
I was able to get it to stop by leaving the configuration profile in the JSS (you can upload it if it's not already there), then setting it to be available in Self Service scoped to all users and all computers (or devices) with NO category selected. This way the JSS sees that the device is allowed to have that profile and won't try to remove it automatically. Since there isn't any category selected, the end user won't see the profile in self service either.
Hopefully this helps in your situation! Let me know if you would like a screen shot of the settings I have in place for one of our configuration profiles.
@slinxy take a look at this [https://www.jamf.com/jamf-nation/discussions/25665/change-in-smart-mobile-device-group-membership-pulls-config-profiles-9-101](link URL). it's garbage. you don't mention which version of the JSS you're running but I'm willing to guess you're being impacted by this product issue, which will be fixed with V10 (and who knows what that might break because this was working fine before...).