That should be working as intended.
https://gyazo.com/7ab140bfa046cb5082b7c974b62f613f
Viktor's E
ACTIVE: Viktor deploys a gravitational imprisonment device at the target location which arms after a brief delay. For 4 seconds, the trap Slow icon slows all enemies that pass through its field, persisting for 0.25 seconds after leaving.
Whilst under the trap's effects, enemies generate a stack every 0.5 seconds. At 3 stacks, enemies are Grounded icon knocked down and Stun icon stunned for 1.5 seconds.
Think about it this way. Viktor's E slows like a Lux E, which is in an AOE. Viktors E also generates stacks, similar to how Kennen's ulti applies stacks of his passive. Viktor's E works as if it's a Lux E with a mini-Kennen ulti going on in the same area. Upon reaching the required number of stacks, you are stunned. Think about Viktor's E as an ability with 2 effects, rather than an ability that causes an effect, which is tied to another effect.