A recent article by CBS Sports' Matt Moore focused on the Spurs' defense with Kawhi Leonard on and off the court. The findings were surprising: San Antonio defensive numbers are much better when Leonard rests.
Moore explains why that might be. You should really, really read the entire article because it's great, but the gist of it is that opponents put Kawhi's man in a corner and go 4-on-4.
That seems to explain why units featuring the two-time Defensive Player of the Year are not doing so well on defense. The question that is still unanswered, however, is why are units not featuring Leonard excelling on that end.