Were they using their USM hilts?
Yep Kavar had both sabers when I fought him but the option to "loot" him never appeared. It did that last time I got to final dant. with 2 Jedi Masters, neither one dropped the sabers for looting. Both had them though
EDIT: It is fine however if I just kill them when I find them right off hand. When I kill Kavar he drops his sabers on Onderon only at the end of Dantoonie does the option to loot them not appear.