I can't think of any way how this is a plot hole. At best it's weird behavior, but a little more understandable when you consider she's basically a personal assistant who's being asked to commit her first corporate espionage and gets surprised by the evil menacing antagonist. If she minimized what she was doing, there would be nothing on the screen and it would be just as suspicious. "Oh hi Obby, I'm just sitting here staring at the Desktop icons, don't mind me."
Considering this one follows the new style of over-indulgent lengthy description for a comedic effect, it's a weak critique of an incredibly minor character reaction. Obidiah was already building the suit and planning to kill Tony in order to get the arc reactor in his chest, at most this sped up the plan he already had. In fact Pepper's activities have no effect on the story at all, when she tries to tell Tony he is immediately attacked by Obidiah, thus revealing the betrayal before Pepper shared her intel.
Plot contrivance #1 - Armed terrorists run from one man
The next time someone runs at you firing an automatic weapon, good luck relying on the weapon that's down at your side and NOT ready. The 1.5 seconds it takes to switch off the safety and lift it up to aim is plenty of time for a few bullets to penetrate your chest. Since there was no cover, the terrorists were put on the defensive and were likely surprised. These aren't swords that require close proximity, self preservation isn't a plot contrivance.
Unaddressed Issue #1 - Why couldn't they just speak English?
That's a pretty short-sighted stance to take that perpetuates the notion Americans think the world should conform to them. Why couldn't Obidiah learn Arabic? The video wasn't already translated, so perhaps he does. Just because one of the terrorists speaks English, he may not wish to make a recording using the language of Western infidels even if they're business associates, preferring to stick to his native tongue while in the presence of his own people in his own country. Also it keeps Tony in the dark so they can control what he knows.
Most of the initial articles were pretty accurate and succinct, lately the descriptions are getting really really long, involve outlandish references, and are mostly nitpicky for the sake of adding a few more items to the list.