So, the problem is that I can't make conflicts based on a misunderstanding that wouldn't resolve in five paragraphs. My chars are too smart for that, I'm too smart for that (and also have all the time in the world). It's not like I wouldn't come up with a solution to the consequences, however, the fact that I can't create this type of conflict is bothering me to no end.
How can I make a long-lasting misunderstanding to build my conflict on? Think about conflicts like X goes after Y because Y stole the MacGuffin from its containment unit, not knowing that it would mean the end of this world as I knew it, but Y thinks that X is just greedy. Note: this would work out if it wouldn't be for those meddling main characters!
Also, using my questions as an example is right out, please.