It was a joke. Shane told you upfront, and you still got fooled. Watch for the question, "How did you know it was a joke?" The technician looks to Aaron, who in turn gives a slight shake. No answer, not in front of Aaron. Blame Abe. He fell for the red herring, therefor everyone else did. Originally, Aaron may have put the fungus there as a joke. True, the original time line #2 has been replaced and the first play of it can not be truly known. The truth is, Abe discovered this that the box was causing time travel, built two boxes, and Aaron came out without Abe's knowledge. Very likely, Abe may not have even finished the second box yet. As soon as the first box is working and turned on, someone will exit.
How did the fungus not prevent Abe from climbing in the box? It should have left Aaron in complete control. Granted, in an earlier concept, Aaron(1) could be clueless. The technician would not know that there is an Aaron(1) and Aaron(2). Thus, in front of Aaron, the technician does not give an answer to Abe’s question. In the original time line, Aaron(1) may have planted the fungus as "a joke." or Aaron(2) could plant the fungus which would make Aaron(1) innocent, surprised, and clueless.Since we don't know when Abe built the box, its hard to know for sure. We see, however, that Aaron is 'finding out' this information allegedly the day after Abe finds out. This is hard to believe Abe, since if he just found out, how would he have had time to build the box already? Abe is not being completely honest.
So Abe’s first reaction was correct, "What did you do to this thing?" Part of the proof that we are watching Aaron(2) or Aaron(3) is the joke that Aaron starts to tell in his office. Thus, proof of the time loop, whether Aaron repeats this joke from memory or a recording (in the time line, he hasn’t heard it yet). There can be no debate though, Abe is definitely talking to an Aaron who has traveled back in time.
What does the fungus accomplish? It insures that Abe will build and store his boxes in the U-Haul storage center, a climate-controlled environment.(Since no fungus is found in the larger boxes, one can say that it was not in the experiment from the time travel itself.) It is certainly safer out of town so that no one may see them and their doubles. This step is essential to their success. It may also be an attempt to convince Abe not to get in the box (from Aaron’s perspective). This would allow Aaron sole control over the boxes. It is easy to believe that Aaron hasn’t traveled in time yet, because Abe is still under that belief. It is very hard for many people to grasp this on their first viewing, even after reading the explanation. But, Abe built a box early on. Long before most fans realize it, even after several viewings. How else would he know about the shock and other details if he had only made one experimental trip? When would he have had the time to make rules and plan the oxygen and the timing? Abe is tricking the audience, because he is misleading Aaron.
