Why does Aaron Cross lie about being out of medication?

Aaron Cross was afraid of running out of his stock and reverting to the significantly less intelligent person he used to be. Later in the film Marta is asking why the meds are so important to him and he shows her a picture of himself and says:

This was me... Was... My army recruiter was looking to make his quota. He added 12 points to my IQ... 12 Points to make the minimum...

He didn't have a substantial stash as it was anyways. He had only a few blue pills (the ones most important to him because of their intelligence enhancement) and no green pills (which he no longer needed, but he didn't know that). When he finally tracks down Marta he tells her he hasn't had a green pill for 50 hours. At that point he only has 1 or 2 blue pills left.

He knew he was running out, that is why he told the agent he needed more. He also comes across as something of an addict. He'll do anything to get his fix; lie, cheat, murder, anything...

+ Although the U.S. military does not test IQ they do administer the ASVAB, 
which tests basic math and reading skills. There is a minimum score a 
candidate is expected to get to enter into the military. 

It's explained in a deleted scene. ALL the agents were suffering from paranoia. They were each stashing extra pills, money and false IDs. That's why Aaron had that huge stash of money and IDs conveniently tucked away. If they'd kept the scene it would have explained a lot. There's actually a few deleted scenes that fans of the movie should watch.

I think Aaron is stockpiling his meds because he is suspicious something foul is afoot. With his enhanced mental capabilities, he is very perceptive and must have some inkling that something doesn't smell right ... a sort of sixth sense. He says he's not sure if his log cabin contact is supposed to kill him or give him a pep talk ... I think he feels something is wrong and is preparing for the worst by making contingency plans to go off the grid again if necessary and go on the run as Jason Bourne had to do.

Later in the movie we discover that some pills were a way to control agents. Guess Cross lied to hide a couple of pills and protect himself in case of lack of medication.

The reason that Aaron Cross lied to the Outcome agent in the cabin to get more pills is that he was already being punished, thats why he was in Alaska on a "training Mission". He had gone off the grid for 4 days because he killed some innocent people due to bad intel on an assignment. Thats in the flashback with Erick Beyer So Aaron thought that it was likely that he would have to run even before the Jason Bourne fiasco made Outcome a liability. He was trying to get some pills so he could have a chance to escape. Also he probably didn't like being on a such a short leash. Of course he fears a cognitive downgrade to 12 Iq points past normal, as that would put him in the mentally retarded category and he would need to live in a group home. Most people would do anything to prevent such a fate. Its not an addiction to simply want to be a functioning human being capable of independent living. I find that analogy very upsetting myself.

This is in response to Mathew Foscarini who suggested that Cross was unaware of what the pills did until Dr. Marta explained their use. When Cross 1st entered the cabin and explained what his prescription was, he referred to the pills as "phys. meds 250 green, cognitive programs 400 blue." I subscribe to the theory that he crossed the mountains in the fastest way possible because he was aware that he had 2 days remaining so it was important to shave those days off the trip and secure a new supply.

There are two types of pills in that movie. The green ones are the pills that enhance his physical abilities. Aaron Cross' physical abilities were now permanent and he didn't need the green pills anymore. The blue pills give him the enhancement in intelligence. He still needs the blue pills in order to preserve his superior intelligence. He meets Rachel Weisz's character who can help him viral off the blue pills. What does viraling off mean? It means you don't need to take the green pills or the blue pills everyday in order to retain your superhuman abilities. That is why he goes to the Philipines, because he won't have to rely on the blue pills anymore.

we see him "chem" twice on his journey so it seems he is double dosing so he hides his pack so he can say he lost them in order to get more, So when Cross he virals off them, as he has no way of getting more pills detox was inevitable, and to detox with out the stem injections would have taken days/weeks the injection sends him in to rapid detox which clears his system in a much quicker time than naturally detoxing would, Once his system has beaten the virus the addiction is gone and the after effects of the pills are gone along with the added ability's to