I think the issue is that, ordinarily, a sitting Cabinet member who is requested to speak to the FBI in connection with a pending investigation would have a lawyer present to represent the executive branch of the government. White House counsel is not personal counsel for the cabinet official (or president), but instead represents the office of the president/executive branch. President Trump, for example, does not have any executive privilege that he can personally assert; instead, because he is president, the White House can, and does, assert that privilege. Representative Issa either doesn't understand the distinction (unlikely), or he is stirring the pot (likely).
General Flynn has pleaded guilty, and his attorneys have characterized his actions as an uncharacteristic lapse of judgment. The government has indicated that he has satisfied his obligations under his plea deal and advised that it doesn't are if he gets prison time, or not. We'll see what happens, but I would be surprised if the plea is tossed by the Court (particularly because Flynn himself isn't really advocating for that).