I prefer Champions of the Just all the way, but I did forget her involvement in the Calpernia arc.
So that's one moment of competence, at least, though Calpernia notices the suspiciously returned crystal almost immediately.
My headcanon is that Leliana does in fact run an extremely tight ship when it comes to Skyhold security. I imagine that early on, some of the inner circle may have grumbled a bit about it, but she's bound to have a million and one anecdotes and other ways of proving her point, and everyone acquiesced more or less quickly. Really, a rising world power on the vanguard of the battle with evil needs super-tight security. Not just to protect themselves from that enemy, but from supposed "allies" as well. Everyone is bound to want eyes and ears in Skyhold for their own ends, and we can't afford that.
I'd have liked a cutscene or at least a standard conversation that shows successful anti-infiltration measures from Leliana and her agents, as well as admonishments from her to double their vigilance instead of thinking the enemy will give up.
@thats1evildude: Agreed on Solas. It is rather suspiciously convenient that the one mage who has any useful insights on dealing with the rifts and the Anchor just happens to be right there when the Conclave is blown off the face of the planet. But Solas is likely an expert liar and manipulator (I don't think the elves' view of him as a deceiver and trickster is altogether wrong, even thought his "portfolio" among the old pantheon was actually rebellion) and his current persona is so outwardly unassuming that pinning anything on him, or just tracking his recent pre-Conclave movments, is probably impossible.