When President Carter took on the defense establishment in Congress two weeks ago by vetoing the military procurement authorization bill, he said one reason was to restore some cuts that the legislators had made in "the muscle of our military requests."

Now it turns out that some of those cuts had already been agreed to by the Pentagon; others were merely shifts from one part of the defense budget to another; still others were deferrals of items that Congress promised to approve if needed later.

Additional items on the president's list were indeed cut out by Congress. Several are major.But even presidential aides acknowledge a number of others are minor.

Carter cited the cuts in his veto message as a type of offset to his main objection to the bill: the $2 billion nuclear-powered aircraft carrier he opposes as wasteful.

Had he cited only the carrier, Carter - who has also acted to stop production of the B1 bomber and neutron warheads - might have been exposed to charges he was weakening U.S. defenses. As it was, he could say he was working to restore funds to "critical areas," and for "more immediate improvement in our defense forces."

But a growing number of Congress members and senators are now saying, as politely as they can, that the president made "mistakes," that he was "misinformed."

While House aides yesterday defended the president's veto message. Gerald Rafshoon, who is mainly concerned with the president's public image - and who some have said advocated the veto as a way of portraying the president as dealing forcefully with Congress - said "it was not just talk. Congress had cut muscle for another layer of fat."

But at least one administration official, going over programs that were cut and listed in White House documents as critical and in line for restoration, said, "Maybe one or another was not a particularly good selection."

The president accused Congress of slicing $500 million from "readiness funds . . . which are not glamorous but which provide the immediate fighting capability of our forces . . ."

An Office of Management and Budget paper lists among "the readiness cuts which "should be restored:"

$57 million for reenlistment bonuses," a key to retaining skilled people."

These funds for fiscal 1979 were cut by the House Appropriations Committee in a dispute with the Pentagon over whether to change the bonus system, not to cut it back.

Both Congress and the administration want to continue bonuses. The Pentagon, however, wants to pay a lump sum of $2,500 to a service person at the start of a reenlistment period; the House committee wants to continue paying $3,000 over three years.

$155 million cut from the multi-billion-dollar military supply and stock fund activities.

Here the House Appropriations Committee made an arbitrary $50 million cut for each of the three services supply agencies plus $3 million from the Marines Corps and $2 million from the other Defense Department agencies.

The committee added, however, that it would permit reprogramming of the funds if any service could show the reduction "will have an adverse effect on military readiness."

A Carter official yesterday defended including this cut as necessary for restoration on the ground that reprogrammed money would have to come from some other unnamed account.

When the president referred to the readiness area in his veto message and press conference, he listed "training of personnel" as one area where cuts had been made. No such cuts appear in the OMB paper nor did officials there questioned yesterday know to what area the president may have referred.

Carter also referred in his veto message to elimination of $800 million of a $1 billion increase he sought for Army weapons and equipment. These additional funds, the president said, were needed particularly for "NATO-oriented forces."

The largest items identified by OMB in this area were:

$353 million in ammunition. The House Appropriations Committee cut this amount from the original administration request for $1.4 billion.

The committee found $26.6 million here for training ammunition where the Army already had enough rounds for more then two years of operations. The Army itself decided it did not need an additional $12.3 million in this category after the budget had been submitted.

The Army also informed the committee it couldn't use in fiscal 1979 $37.6 million for a new laser-guided artillery shell called Copperhead and those funds were deleted. That money too turned up on OMB's critical cut list.

Another area of congressional cuts that drew Carter's criticism was research and development. Here the president said he had sought "a substantial increase . . . to sustain our position of technical excellence . . ." but the cuts "could lead to an actual decrease in these funds for next year."

The OMB backup papers say 3 percent real growth is needed in this category and criticized Congress for deleting $800 million in administration programs while adding back $400 million of its own.

Among the reductions listed for restoration by OMB are:

$10 million for an Assault Breaker program to be used in NATO defense. Congressional sources say this program in fact was not cut, only transferred from the military service accounts to the Defense Department's Advanced Research Projects Agency.

$32 million for development of planes that have vertical take-off and landing capability. These funds, congressional sources say, were cut from a program that the Pentagon has backed away from. Instead, a greater amount was put into research on a newer, supersonic version of the same plane.

Sen. Thomas J. McIntyre (D.N.H.), who chairs the Armed Services research subcommittee, said last Friday that the vetoed bill would permit "at a minimum . . . between 1 percent and 2 percent real growth" - not far from Carter's target and $200 million in a $12.25 billion account.

Within the president's and OMB's lists there are several programs that some members of Congress agree should be restored. These include $15 million for operating the North Dakota perimeter acquisition radar station that once was part of the antibalistic missile system. It is being stepped up in quality to be used to determine the size and intended targets of any Soviet strategic missile attack.