What is this symbol used in Kabaneri of the Iron Fortress?
According to this post on the official website, this is the 浄化マーク, meaning "purification mark". It is derived from / inspired by older variants of the character 六, which is the "Rok-" in the phrase "Rokkon Shōjō" and means "six". This symbol is written on things to indicate that the things in question are "pure" (free of kabane, presumably). 

I don't recall this being mentioned in the anime.