Is there anything I can do to stop a Codex from cloning?

• Use flashbangs. Disorientation caused by flashbangs will prevent them from cloning, as answered before.
• Codex can also be stunned. Examples include Arc Blade attacks(note, however, that it has a fairly low chance of 25%).
• Codex registers as mechanical with respect to EMP grenades and Bluescreen rounds. If you have appropriately high tech level, then you could rather try suppressing that thing FOREVER. A shot from a Plasma Lance with a Bluescreen round will instantly kill it if the hit is delivered properly.
  • Codex can still clone itself when it is at HP 1, but this will result in the source being killed. This will degrade the cloning attempt into teleportation.
  • Although they COUNT as multiple attacks, damages from multi-attack abilities (Rapid Fire, Chain Shot, Fan Fire) are resolved at once. Therefore, if a Codex dies from such an ability, it does not reproduce, even though it had received multiple hits from the attacker.
• Certain Psi abilities are possible to hinder a Codex. Examples include Stasis, Insanity, or Void Rift. You can even try Dominating it. (Note, however, that a dominated Codex does NOT replicate.)

I just learned this from some players chatting in a Twitch stream. You can actually disable a Codex's ability to clone itself by disorienting it with a Flashbang grenade first!