Perhaps Donnie's weather machine is only powerful enough to keep the window open long enough for one traveler to pass through then: Ultron?
On a side note, It may be because I'm up too early and somewhat delirious but I just noticed the spelling correction with this Disqus messaging app and I'm enjoying it thoroughly.

In the middle of the episode, Agent Ward lists the items required to create a portal like the one used in New York in the Avengers movie and that the team should erase the specs of these items off the plane's database. If you notice, Ward mentions the gravitonium which Coulson cooly checks off as being off the records…