The first hint is the mentioning of the smell that occurred. Faulkner brings this up pretty quickly in the story, only after mentioning her death and her vanquishing of the tax alderment. There is a long passage that describes the smell emanating from her house, which started "a short time after her sweetheart--the one we believed would marry her--had deserted her". The clues are there, we just don't see the connection quite yet. The next hint is the fact that after her father died, she was in complete denial and wouldn't release his body. She "did that for three days" before "she broke down" and allowed them to take the body away. Again, not a connection to be made yet, but definitely hints at her disturbing tendency to hang on to dead bodies for a long time, and be in denial about their deaths.
The most obvious hint comes when she buys arsenic, and then Homer Barron disappears soon thereafter. It is then that we can start piecing things together; we can assume the arsenic was for him, that the smell was him, and if we are very insightful, make a connection between the toiletries she bought for him, and her father's death, and maybe draw conclusions.
Those hints are there, and especially clear after a second reading of the story; with a first reading it is more difficult, but that is why it is such a killer ending. :)