Jews have a tradition of placing stones on the grave. In the Film Schindler's List, in the ending scene everybody places stones on the grave of Oskar Schindler. But Liam Neeson places a pair of roses on the grave and stands over it. What does this signify?
According to the movie's FAQ on IMDB.com, Neeson's reason was "for respect and the fact that he was proud to portray such a historical figure."
Also, the scene shows actual Holocaust survivors as well as the actors who played some of them. I believe it is only the survivors, not the actors, who place stones on the grave. So perhaps it would not have been proper for Neeson to place stones on the grave, leading him to use roses instead.
The previous answer is good, but for a little more detail of the tradition of leaving stones, here's my two cents.
Jewish people leave stones instead of flowers for a variety of reasons, many with Talmudic roots that I'm not educated enough to explain. For a more complete explanation visit Mi Yodeya, the Judaism SE. However, one of the primary reasons is that stones offer permanence and solidity. They are a standing testament and remembrance. Unlike flowers, they don't wither and need to be removed or replaced. They become part of the monument.
Neeson may have felt that both due to his non-Jewish identity and the fact that he is an actor, not a survivor, that it was inappropriate for him to leave a stone and permanently alter the gravesite. Flowers are a good alternative for him to pay his respects in a less invasive way.