Then of course was the clandestine American commando raid that killed Osama bin Laden for which the Pakistani authorities weren't notified beforehand and which they and the Pakistani people considered a breach of their territorial sovereignty.
But the incident which is creating the current "diplomatic imbroglio" between the U.S. and Pakistan was the U.S. missile strike that killed 24 Pakistani soldiers at a military outpost in November. The U.S. called it an unfortunate accident, but he Pakistani's weren't buying it. They reacted immediately ordering the U.S. to cease such attacks and then ordered the closure of all the main U.S. supply routes leading into Afghanistan. In current diplomatic meetings with the U.S., Pakistan has demanded an apology by the Obama administration for the killing of the 24 soldiers before it will consider re-opening the supply routes. The Obama administration has refused to grant the apology, primarily citing the April 15 Haqqani Taliban attacks on the American military "reportedly" launched from areas within Pakistan as their primary objection and thus the current diplomatic standoff.
Yet if one were to look dispassionately at this impasse, it becomes clear that the U.S. obsession in pursuing purported terrorists everywhere, but particularly in Pakistan, going about it with remote controlled drone strikes and missile attacks that kill innocents, with no regard for Pakistani territorial sovereignty, coupled with the seeming immunity from prosecution of those who have committed crimes against its people, has inflamed the indigenous population in Pakistan which refuses to accept silently what they consider obvious injustice and effrontery committed by the U.S. on Pakistan and its people.
Add to this volatile mix, Obama being in the midst of a re-election campaign, worried over being cast as soft on terrorism and not tough enough on Pakistan for providing sanctuary for "terrorists" that incessantly comes from the far right reactionaries in the Congress, he's caught in the paradox that even an apology to the Pakistani's would be seen as capitulation and weak kneed appeasement.
This is the type of absurdity this president finds himself in, being engaged in an unnecessary war and obsessed with terrorists and terrorism becomes a main pre-occupation that interferes with his other pre-occupation; getting re-elected.