Hi,
I think it's a bug - AD Group Discovery will write DDR and thus create AD objects in SCCM DB which are rejected by AD System Discovery.
adsysdis.log
ERROR: System testcomputer is a unsupported operating system, unsupported version, or malformed AD entry. Reported system type is: ().
adsgdis.log
INFO: DDR was written for system 'testcomputer' - <path>\inboxes\auth\ddm.box\adhszouf.DDR at 9/11/2015 16:50:1.
I've found this post where the same behavior was considered as a bug in 2k7 and hoped for a fix... well the fix is still not there.
Additionally I raised this as a feature request for vNext... thogh I hope someone has a workaround to prevent this behavior...