Bumping this for visibility as Kozilek's Command is still heavily bugged. I've had to submit numerous refund requests from leagues just this week due to this issue. Here's what I've encountered so far:
If you attempt to cast Kozilek's Command while the game is lagging, it will often hang once the box to select the modes pops up. You can select the modes, but the "cast" button will remain shaded for an undetermined amount of time, all the while your clock is still ticking down. Sometimes it's a few seconds. Most times it hangs for 30+ seconds. Very rarely, it hangs indefinitely. This can be resolved by restarting the client mid-game. Once you get back into the game, it'll allow you to cast the spell lag-free and with no issues. But this is annoying to say the least, costs valuable in-game time, and some people may not even know what the workaround is. This one is difficult to reproduce reliably and is entirely reliant on how laggy your particular client is at any given moment.
If your opponent casts a spell, tap mana first and then play K-Command. It will auto-pass priority to your opponent and leave the mana floating in your pool. You will be unable to respond to anything until either the end of the phase or until you right-click and select "Turn off Auto-Yields". But in the meantime, the spell that you intended to respond to in the first place was allowed to resolve while you sat there with floating mana. Your opponent will be allowed to cast spells and abilities unimpeded until you either turn off auto-yields or until the end of the phase. Which means he gets to cast whatver spells he can so long as he's fast enough to do it before you can turn off the yields. This can be worked around by making sure you click the K-Command and select the modes before tapping mana, but there are plenty of people who are used to being able to tap first and pay later.
Worse, this happens even if you have K-Command in hand and tap out. Even if you don't click the card or intend to play it. If you have K-command and you tap out in response to any spell, the same thing will happen: You'll pass priority until either the end of the phase or until you're fast enough to turn off auto-yields. As long as you don't tap out, you're fine. But if you decide to tap out while K-Command is in your hand, it'll bug out.
Simple process to reproduce. I have both "Stack abilities Automatically" and "No Possible Play: Yield All" checked.
Step 1: Opponent casts something.
Step 2: Either tap out entirely, or float an amount of mana first, then click the K-Command as if you're going to play it (not necessary if you tap out entirely). It'll auto-pass priority.
Again, you *can* regain control by selecting turn off auto yields, but that takes time and your opponent has free reign of the board until you do. Making sure to click your spells before paying for them helps in some situations, but there are other situations where floating mana for later use is the correct play to make, and the current bug prevents you from doing so.