One theory could be that Dosan's corpse was cut in to pieces by Yoshitatsu's soldiers who claimed they were the one who killed Dosan. If that is correct, then there should be more graves. Here is how Dosan was killed according to the Shincho-Ko ki, p. 103 Elisonas/Lamers (Gyuichi).
"Nagai Chuzaemon took on Dosan, laid hold of him as he was raising high his assault sword, and locked him in an embrace. Just when Nagai had almost succeeded in taking Yamashiro Dosan alive, Komaki Genta, a ferocious samurai, came running up, mowed down Dosan crosswise at the shins, and took his head as he fell prostrate. Chuzaemon, keen to get some evidence for later, sliced off Dosan's nose and made off."
Saito Dosan was an interesting and colorful figure in my opinion. If there are more of his graves/tombs scattered around Gifu City, I would like to know.
Tenka no tame!