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.
If you watch the end closely you will notice that both the Schindler Jews and their actor counterparts place stones on the grave. We only see Liam Neeson's forearm and hand as he places the two red roses. I believe Neeson uses roses to show his respect instead of a stone and he knows his portrayal is as temporary as the flowers. Red was used as a connection to the little girl in red who symbolized the innocence and death of the 6,000,000 Jews butchered by the German Nazis.
The roses places by Liam Neilson are out of respect for the man he portrayed.It doesn't signify much more than that. A man paying his respects, as we all should (and we may even say on our behalf as an audience) to Oskar Schindler.
The stones are stones of rememberance. It is a Jewish custom daiting back to the book of Genesis with placing stones as a marker in a place where something happened to remember the event. They are also placed on graves as a form of rememberance for that person. The stones recall or commemerate a person's life and deeds.