It's also important to note how politically convenient it is for the US government to blame instability on Iran. If Iranians are causing the mischief, then it's easier to a) manufacture a reason for hostile action, and b) explain away the utter failure of the United States to quell the insurgency or win the support of the populace.I think Steve Gilliard was the first person I read who pointed out the flaw in this logic: the Iraqi-Arab tribal structure is notoriously suspicious of outsiders, and immensely conscious of who outsiders are.
So, if Syrians and Iranians are coming, in large numbers, to Iraq and starting shit (IEDs, decapitations, whatnot) that's a problem. But the fact that a) the Iraqis must know who they are, and b) are abetting their activities by silence or active participation, is much, much, much worse. If the Arab Shia in Iraq are willing to work with the Persian Shia of Iran, that's a sign of just how much the Americans are hated by the Iraqis not a sign of poor border control.
The situation in Afghanistan is a bit different, because the Pakistan/Afghan border runs straight through Pashtun lands -- the problems in the south are largely fueled by Pashtun solidarity, if I'm reading accurately.