Alcohol
Alcohol is a very complex symbol in the novel. Obviously, it is a metaphor for the “whiskey priest” and his tragic character flaw. Alcohol is also the object of an attempt at prohibition-style laws which situates it as a symbol of every manner of sinful behavior which simply cannot be eradicated through legislation, even legislation at the point of a gun. But alcohol is also a necessary component for doctrinal sacraments in the Catholic ritual, so alcohol also takes on a positive symbolic element that unifies the sacred with the profane.
Morse Code
Coral Fellows and the Whiskey Priest on the run are separated by profound ecclesiastical differences on account of her being Protestant. (Though she is Catholic-curious!) She makes the effort to teach him rudimentary Morse Code to facilitate communication and a larger and more symbolic sense the Code becomes the means by which they reach across that spiritual divide to connect.
The Crippled Dog
The image of the starving priest struggling with the crippled dog over a bone with pitifully little meat left on it lends the novel a philosophical dimension in a subtly symbolic way that avoids becoming too intrusive or overbearing. The image of the fallen priest and the handicapped dog struggling over such a paltry bit of flesh harkens to the Catholic sacrament of eating consuming the flesh of Jesus. The beauty of that symbolism is that it then opens up to become a more expansive metaphor for the age-old question of whether man is a higher being or merely an dumb brute animals just looking to survive like every other mongrel on the planet.
Vultures
The vultures appear at critical junctures in the story and keep popping up throughout the narrative. Like alcohol, the vultures are a bit complex. Their first appearance is appropriately ominous and creates the dark mood typical of vultures being a portent of death. As they continue to show up, however, they subtly take on a greater dimension in which the portent of death can also be interpreted as meaning the natural course of resurrection and rebirth appropriate to a story heavily invested in Catholicism.
Faith
The author, Graham Greene, has himself admitted that he intended faith to be specifically and explicitly be viewed in this story as a symbol of resistance to the threat of fascism which was very prevalent and very dangerous at the time and which seems to be making an inexplicable comeback in the 21st century. The power of faith to compel the opposition to systemic fascism according to Greene is its moral superiority. The book attempts to work out through the story of the fugitive priest a means by which the adoption of a strong moral foundation built on faith serves to obstruct the path and strength of fascist empowerment.