The special U.S. envoy to Central America, Richard Stone, today ended inaugural talks with the Nicaraguan leadership that skirted the rancor of recent days but appeared to leave Washington and the Sandinistas locked in antagonistic positions.

Stone said the main U.S. problem with Nicaragua's revolutionary government stems from Sandinista support for "guerrilla movements in other countries," a clear reference to the Salvadoran civil war that is the focus of his mission. He then departed for Guatemala, where he arrived after a brief flight.

Daniel Ortega, head of the three-man government junta, said after his talks with Stone last night that Nicaragua's main problem is that the Reagan administration has chosen "the way of war" in an effort to "overthrow the Nicaraguan people or bring them to their knees" by backing antigovernment guerrillas.

Both sides thus restated their positions in a public reflection of what informed sources said went on in Stone's private conversations with Ortega and Foreign Minister Miguel D'Escoto. But the sources said there was no unpleasantness in either meeting, even though the visit was preceded by mutual recrimination from Managua and Washington over last week's expulsions of diplomats from both sides.

At the same time, they added, neither Stone nor the Sandinista government presented any new ideas for relaxing the tensions that have reached their highest point since Sandinista revolutionaries overthrew the U.S.-backed dictatorship of Anastasio Somoza in 1979. This seemed to leave the standoff as it was before the envoy arrived yesterday morning, just short of a break in diplomatic relations.

The Foreign Ministry, for example, lodged a formal protest with the U.S. Embassy over what it said were:

* Attempts by U.S. authorities to confiscate a diplomatic pouch addressed to the closed Nicaraguan consulate in New Orleans.

* Refusal to allow Nicaraguan diplomats to enter the closed Nicaraguan conslutate in Houston and retrieve documents.

Both actions, the ministry charged, violate the Vienna Conventions on consular and diplomatic treatment. It demanded they cease "immediately."

Aside from Nicaragua, Stone offered an indication he might be planning talks with the Salvadoran opposition. He called the idea "of great importance." While refusing to reveal his plans, he added, "I am going to address it."

Other reliable sources said U.S. officials in Stone's entourage have been in at least indirect contact with the Salvadoran opposition as part of an invitation for talks launched Thursday in Mexico City by the Revolutionary Democratic Front and the Farabundo Marti National Liberation Front, the Salvadoran political and military opposition groupings.

Stone's inclination is to go ahead with such talks as part of his congressional mandate to seek peace in El Salvador, the sources said. But they underline the political sensitivity of the idea because of resistance from the Salvadoran right wing and some officials within the Reagan administration.

The outgoing U.S. ambassador to El Salvador, Deane R. Hinton, urged "dialogue" between the Salvadoran government and Salvadoran leftist groups last fall. That idea was angrily rejected by the chief Salvadoran rightist leaders.

Thomas O. Enders, outgoing assistant secretary of state for inter-American affairs, was later reported considering a two-track policy of military aid and efforts to talk with the left, at least as a way to deflect congressional criticism.

But Enders and Hinton have lost their jobs since then in what has been portrayed as an effort by harder-line administration officials to gain control over U.S. Central American policy. Against this background, the proposal for direct talks between Stone and the Salvadoran opposition becomes even more delicate.

The informants pointed out, however, that Stone would not be facing suspicion from President Reagan's advisers as did Hinton and Enders because the former Florida senator, known for his conservative Latin American ties, "is one of them."