A Jan. 12 telephone call from his former Deputy Attorney General warning President Carter against the "terrible mistake" of firing U.S. Attorney David Marston in Philadelphia was the product of a full year's application of incompetency and naivete within the Carter administration.

Whether the warning from Peter Flaherty was relayed to the President is doubtful, but it was ignored anyway. More significant, however, are questions raised by the fact the call was made: Why was Marston, a Republican political appointee, kept on for a full year? Why was he then marked for dismissal after building an impressive record?

As with questions posed about Richard Nixon in the early unfolding of Watergate, there are alternative answers: conspiracy or incompetency. The evidence here is overwhelming in favor of incompetency, which has now turned a trivial patronage squabble into a nationally publicized crisis.

Candidate Jimmy Carter's pious compaign promise to install a nonpartisan merit system at the Justice Department forms the base of this problem. However, a general decision made a year ago to purge Republican U.S. Attorneys effectively finessed the wholly impractical campaign pledge. Actually, with no reputation and only six months in office, Marston posed far less trouble than the sack of experienced Republican prosecutors in Michigan and New Jersey.

But nothing was done. The reason was not Marston's skill but Justice Department lassitude, in Philadelphia as elsewhere, about finding a successor. Over luncheon with a friend last June, Attorney General Griffin Bell and his lieutenant, Associate Attorney General Michael Egan, called Philadelphia politics a "jungle" where agreement is impossible.

The delay transformed Marston, 34, from expendable to untouchable when he became the first federal prosecutor to attack Philadelphia's political corruption. Deputy Attorney General Flaherty, teh former mayor of Pittsburgh, explained to Bell and Egan that Philadelphia is a town of crooked Democratic politicians and strongly urged Marston's retention.

But as Marston's office indicted and convicted important politicians, the city's congressional delegation - led by Rep. Joshua Eilberg - pushed ever harder to get rid of him. "Eilberg was the one who insisted," a Justice Department insider told us. "Judge Bell looked on Eilberg as something of a pest." Coincidentally or not, federal prosecutors were moving into the Hahnemann Hospital case involving investigation of Eilberg.

As November began, Marston was invited to a meeting of U.S. Attorneys that excluded some seven of his Republican colleagues marked for dismissal. Then, on Nov. 2, the probe of financial irregularities at Hahnemann Hospital escalated with secret FBI interrogation of a witness in Philadelphia. Two days later, Eilberg telephoned the President and had his call returned.

At Carter's White House, it is nearly impossible for congressmen to reach top aide Hamilton Jordan, but an obscure Democratic machine congressman from Philadelphia gets a call back from the President. That may be surprising, but at least is understandable. Far less understandable is the President's subsequent call to Bell relaying Eilberg's demand. "I admit," a Democratic congressman told us, "with Nixon, I would call it a criminal coverup; with Carter, I am sure it is just naivete."

The mid-November decision to dismiss Marston was so closely held that, when disclosed by the Philadelphia Inquirer Jan. 7, it surprised even Flaherty, now back in Pennsylvania running for governor. With a presidential press conference set for 2:30 p.m., Jan. 12, Flaherty tried that morning to telephone Jordan. Failing, he tried Appointments Secretary Tim Kraft. Failing again, he got White House Counsel Robert Lipshutz just before noon.

"The President would be making a terrible mistake" firing Marston, Flaherty said. Lipshultz declined to tell us whether he relayed that message to Carter. That afternoon the President entered dangerous waters by concealing and obfuscating an essentially trivial matter, ensuring further attention.

The resulting uproar has posed this dilemma for the President: get rid of Marston and thereby guarantee turmoil well into the future or keep Marston at the risk of looking like a pushover for pressure.

Other Pennsylvania Democrats besides Flaherty have told the White House the latter alternative is easily the lesser of two evils, but angry presidential aides do not even perceive a dilemma. Rather, they castigate Marston - calling him "Opportunistic," "phony" and "that turkey" - for embarrassing the President.

In this spirit, the President told freshman Democratic congressmen this week that the Justice Department has found no evidence of any investigation of incumbent Democratic congressmen. In fact, a Justice Department team has found just such an active investigation. So, Carter's misspeaking brought himself more needless trouble, suggesting he is a better crisis-builder than crisis-manager.