Many of the Armor items sold by the Tower vendors have repeat perks. Looks like another copy and paste job slipped through the cracks when The Taken King shipped out to players.
TL;DR Leg Armor sold by the Vaguard have repeated perks. Most of the Bonds, Cloaks, Marks sold by the Vanguard and The Speaker have repeated perks.
Warlock:
Samsara I Leg Armor, Bindcaster I Leg Armor both have perks for Sidearm and Machine Gun ammo, solar agility boost.
Subterranean Bond, Ebonthorn Bond both have focus for scout rifle, shotgun upgrades, Vanguard rep gains.
Ulan-Tan's Burial Ring, The Five Lives of Albios both have focus for Auto Rifles, Machine Guns, Vanguard rep gains.
Haliaetus Bond, Bond of the Tilt both have focus for Auto Rifles, Sidearms, Crucible rep gains.
Titan:
Murvaux Type 0 Leg Armor, Duskrender Type 0 Leg Armor perks for Sidearms, Machine Gun ammo, Solar Double Down.
First Pillar Mark, Tarlowe Mark focus for Scout Rifles, Shotgun upgrades, Vanguard rep gains.
Honor of Cormorant, Moctezuma-Polyphonic focus for Scout Rifles, Fusion Rifles, Vanguard rep gains.
Hunter:
Bog Wild 1.0 Leg Armor, Vermilion Stripe 1.0 Leg Armor perks for Sidearms, Machine Gun ammo, etc.
On the Marsh, End Unsung Hunter cloaks focus for Scout Rifle, Shotgun upgrades, Vanguard rep gains.
We need the basic carry more heavy ammo perk back on Leg Armor. Class items sold need to support more types of weapons.