If my opponent has Vex, Apathetic at a battlefield they control, and I play a Ruin Runner, will the Vex stun the Ruin Runner?

Yes, Vex, Apathetic will stun your Ruin Runner when it is played.

Why this interaction works:

Although Ruin Runner has the ability, "I can't be chosen by enemy spells and abilities," this protection only applies to effects that require a player to choose or target a specific unit.

Vex, Apathetic's ability functions through programmatic selection rather than choosing. When an ability automatically identifies a game object based on a trigger condition (in this case, "when an opponent plays a unit"), it does not require the controller to make a choice or designate a target. Because the ability does not "choose" the unit, it bypasses the protection granted by Ruin Runner.

Sequence of events:

1. You play Ruin Runner.
2. Vex, Apathetic's triggered ability activates because an opponent (you) played a unit.
3. The ability programmatically selects the unit that was just played (Ruin Runner).
4. Because the unit is programmatically selected rather than chosen, it is not considered a target.
5. Ruin Runner is stunned and cannot move for the remainder of the turn.

This ruling is consistent with RiftJudge FAQ #8685, which clarifies that programmatic selection by an ability is not the same as choosing a target, and therefore does not violate protection abilities like the one found on Ruin Runner (or similar units like Baron Nashor).