Iron Man 3 takes place before Thor: The Dark World. We can tell using Agents of SHIELD. The events of Iron Man 3 and Extremis occur before the pilot of Agents of SHIELD. The events of Thor: The Dark World occur about a third of the way through the Agents of SHIELD season.
Given the events in The Incredible Hulk, is it even possible to call Tony Stark without SHIELD knowing exactly where you're calling from? They found an encrypted email to Samuel Sterns and traced it effectively. That's assuming Steve Rogers entirely trusts Stark at the moment. Here, I'm thinking two things. The first is out of universe, but it's the Civil War comic storyline, where Stark and Rogers were on opposite sides here. For an in-universe explanation, he didn't entirely trust Romanoff at first. Stark was clearly involved in Project Insight in helping them build the Helicarriers. That might be a stretch, but it is a possibility. However, the need to keep secrecy, combined with the fact that these events took place over a period of several days (where only the final assault suggested time to contact him), and a final possibility that he has no more suits (at least that they know of) suggests that it is realistic not to contact Iron Man in these circumstances.
Given the events in The Incredible Hulk, is it even possible to call Tony Stark without SHIELD knowing exactly where you're calling from? They found an encrypted email to Samuel Sterns and traced it effectively. That's assuming Steve Rogers entirely trusts Stark at the moment. Here, I'm thinking two things. The first is out of universe, but it's the Civil War comic storyline, where Stark and Rogers were on opposite sides here. For an in-universe explanation, he didn't entirely trust Romanoff at first. Stark was clearly involved in Project Insight in helping them build the Helicarriers. That might be a stretch, but it is a possibility. However, the need to keep secrecy, combined with the fact that these events took place over a period of several days (where only the final assault suggested time to contact him), and a final possibility that he has no more suits (at least that they know of) suggests that it is realistic not to contact Iron Man in these circumstances.