Yes... This is why I believe it's important to consider how a dog would act in the absence of instructions.

Whether or not it's likely that Missile would be rational enough to refrain from immediately accosting Levi, it's a fact that he did. However, it's his actions afterwards that appear to be decidedly... un-animalistic. He was clearly not afraid of Levi - everyone saw how enthusiastically he spoke against him. So why the 'clues' with the pictures and why the wait? Only when you consider the end result does it make sense.

The clues, it seems likely, were planted by someone else. Missile wouldn't have been capable of that much training. Consider, too, that K and Aya did not see who it was who passed notes under the door... but immediately came to the conclusion during the trial that it was Missile. And that must be the explanation for the clues - so as to fool them into thinking they had drawn their own conclusions.