Overlooked in all the discussion over whether national security affairs adviser William P. Clark has wrested control of Central America policy from Secretary of State George P. Shultz is the fact that the State Department also is peeved at the Pentagon's role in the debate.

Specifically, officials at State blame the Defense Department for much of the hostile reaction to the Reagan administration's seemingly hasty moves to hold major Army and Navy maneuvers in Central America.

State Department officials contend that the controversy was the result, in part, of premature leaks from the Pentagon that the timetable for the maneuvers had been speeded up and the size of the forces increased. As a result, the officials contend, the issue burst into public view before the administration had the chance to inform key congressional leaders and prepare its case for the public.

Thus when Shultz went before the Senate Foreign Relations Committee two weeks ago he ran into unusually heavy complaints that members from both parties had not been adequately consulted.

Although aides say Shultz is not opposed to a display of military muscle, they say he thought that Congress needed to be consulted first and that U.S. diplomatic efforts should have been emphasized first.

State Department officials say the Pentagon leaks blunted much of the maneuvers' potential impact by forcing the administration to appear confused about what the exercises are supposed to accomplish.

In addition, State is known to feel that DOD officials compounded the problem by casually portraying the recent hailing of a Soviet cargo ship off Central America by a U.S. guided-missile destroyer as commonplace.

One senior State Department official, who asked not to be identified, charged that such remarks showed an "extraordinary lack of appreciation of how sensitive this kind of thing can be to public opinion." At a time when the administration is trying to show that it is carefully weighing and measuring each of its moves in Central America, the official said, "such comments left the impression that we are being overly aggressive, if not outright reckless."

ARABS AND AMBASSADORS . . . The department's acknowledgment yesterday that Kuwait had refused to accept Brandon W. Grove Jr., a former consul general in Jerusalem, as U.S. ambassador prompted reminders that two other men that President Reagan had proposed as ambassadors were rejected because of Arab animosity toward Israel.

In a controversial incident last year, Morton I. Abromowitz, a career Foreign Service officer like Grove, was rejected by Indonesia, which has a predominantly Moslem population and which professes solidarity with the Arab cause. Although Indonesia never formally specified its reasons, it is an open secret within the department that the country objected, in part, because Abromowitz is Jewish.

Then there was the bizarre case of David A. Korn, another career officer, who two years ago was picked to be ambassador to Mauritania, an African country that is largely Moslem. Korn isn't Jewish, but at the time a David Korn, who is Jewish, was serving as special assistant to then-Secretary Alexander M. Haig Jr.

The Mauritania government, confusing the two and acting on what department sources say was the advice of Saudi Arabia, rejected the appointment, even after Chester A. Crocker, assistant secretary for African affairs, traveled there to explain the difference.

Abromowitz since has become head of the U.S. delegation to the Mutual and Balanced Force Reduction (MBFR) negotiations in Vienna. Korn currently is the U.S. charge d'affaires in Ethiopia.

BE HAPPY IN YOUR WORK. . . To help the new U.S. ambassador to El Salvador get into the swing of things, the department will treat him to a special "roundtable on counterinsurgency" on Thursday. The idea is to give Thomas R. Pickering some ideas on how to deal with El Salvador's guerrillas by getting him together with a specially invited group of State Department, military and academic experts familiar with how it was done in Vietnam and assorted other trouble spots.