Executed command from command block minecart, as player and via /execute with target selector arguments r/rm are counting distance from middle of block instead of position of entity. This is the case of unexpected behaviour of selector r=X.
Example:
Run a command in command block minecart: /kill @e[r=0] when minecart is in center of block. Minecart will vanish as intended.
Run the same command, when minecart is in the edge of block. Minecart will not disappear.
This is inconsistent and should be fixed.

in 1.9 pre 3 r=0 can't kill anything, even an executer and entities in the same position.