These experiments involve marker armorstands – it also affects area effect clouds with zero radius. Most likely the bug occurs due to these armorstands lacking a hitbox.

Setup experiment
In this scenerio the armorstands involved in the testing were obtained as follows:

/summon armor_stand ~ ~ ~ {CustomName:"\"A\"",Marker:X}
/execute at @e[name=A] run summon armor_stand ~ ~ ~ {CustomName:"\"B\"",Marker:X}

Note that the X is either a 0 or 1 depending on the following cases.

Results experiment
We distinguish the following 3 cases

• Case 1: ArmorStand A is not a marker, ArmorStand B is not a marker.

  execute at @e[name=A] run kill @e[name=B,distance=0]

  Kills B, works as expected

  execute at @e[name=B] run kill @e[name=A,distance=0]

  Kills A, works as expected

• Case 2: ArmorStand A is a marker, ArmorStand B is not a marker.

  execute at @e[name=A] run kill @e[name=B,distance=0]

  Kills B, works as expected

  execute at @e[name=B] run kill @e[name=A,distance=0]

  Does not kill A, does not work as expected

• Case 3: ArmorStand A is a marker, ArmorStand B is a marker.

  execute at @e[name=A] run kill @e[name=B,distance=0]

  Does not kill B, does not work as expected

  execute at @e[name=B] run kill @e[name=A,distance=0]

  Does not kill A, does not work as expected

Further research
I've had a talk about these seemingly bugs with SkylinerW who in the MC community is a well respected modder/'expert' on Minecraft. This talk can be found back in this reddit topic:
https://www.reddit.com/r/Minecraft/comments/3cgck7/the_nbt_tag_marker1b_made_a_position_glitch_of/

Here are some extracts from our conversation that might help you guys further, credit to SkylinerW:

"That one definitely seems to be a bug. It's not just armor stands, but any entity that is in the ground; I can't get the command to work even if there's a villager with its feet stuck in a block directly underneath the armor stand without increasing the radius to 2 (r=1 still presents the problem, so it's not restricted to r=0). It's specific to the Y coordinate, so it seems like their interpreted location is being skewed for being within a block. I imagine the eye height for marker stands being at the exact Y value causes it to be seen as being within a block.

Code analysis by marcono1234 can be found in this comment.

Also this can be more easily tested with this being run in chat while you don't move:

summon armor_stand ~ ~ ~ {NoGravity:1b,Marker:1b,CustomName:"\"c\""}
say @e[distance=0]

this'll only show your name and not the armor stand's, unless you change it to Marker:0b