A photograph on last week's cover of Newsweek magazine has caused a minor stir during President Reagan's trip to Europe because the photographer placed West German flags on the ground near an SS grave for the picture.

Gary Gerard, director of communications at Newsweek, said the magazine "certainly meant no disrespect" for the German people by using the cover photo by Regis Bossu of Sygma showing the grave of SS man Heinrich Muel- ler with two small West German flags crossed at the top of the stone.

"We wouldn't want to characterize the photo as faked," Gerard said. "Some discussions were held between one of the editorial people here and the photographer overseas regarding the most meaningful way to visualize the fact of the cemetery . . . and some way to visualize the problem of German-American relations.

"The end result is that the photographer who works for the Sygma photo agency went and took it upon himself to try to visualize it the best way he could," Gerard said, adding later that, "In the course of these discussions with Newsweek , it was likely he was told, 'Yes, please get a shot of flags on graves.' "

A White House official said West German government spokesman Peter Boenisch raised the issue of the Newsweek cover photo with White House spokesman Larry Speakes, calling it an example of the "rather sensational treatment" Reagan's visit today to the Bitburg military cemetery has drawn in the United States.

Later, the official said, West German Chancellor Helmut Kohl cited it as an example of sensationalism when talking with Reagan. The president reportedly called Kohl's comments "interesting" but said he didn't know whether the photo had been contrived.

Bossu told The Boston Globe that he "put the flags there myself" as a "symbolic gesture."

"The magazine asked me to put the flags on the grave," he told The Globe. Bossu said the flags came from Bitburg mayor Theo Hallet, who gave him the flags and then objected to his placing them over the SS grave.

West German officials also said television networks had moved flowers in the cemetery to the SS graves in order to get better film.

Last week's issue of West Germany's leading weekly news magazine, Der Spiegel, also carried a cover photograph of the Bitburg military cemetery.

Planted close to two gravestones was a small American flag.

The flag stood close to the graves of Pvt. Alfred Mertz, who died in October 1944 at the age of 17, and SS man Heinrich Mueller, who also died in October 1944 at age 26.