J.K. Rowling thought of everything.
The first time Snape speaks to Harry, he asks "Potter! What would I get if I added powdered root of asphodel to an infusion of wormwood?"
According to the Victorian Language of Flowers, asphodel is a type of lily meaning 'my regrets follow you to the grave' and wormwood means 'absence' and symbolizes bitter sorrow. So we could interpret the meaning of Snape's question as "I bitterly regret Lily's death".
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In Philosopher's Stone, the Weasley twins managed to hit Quirrell in the back of the head with snowballs.
Meaning they hit Voldemort right in the face.
The entrance to Dumbledore's office...
...is literally a Griffin door.
Many believe Hedwig's namesake Saint Hedwig is the patron saint of orphaned children.
But she is actually the patron saint of dead children (St Jerome Emiliani is the patron saint of orphans). Looked at this way, perhaps Rowling named Harry's owl Hedwig to signify she was there to protect him from death... or perhaps it was a clue to Harry's eventual fate in The Deathly Hallows from the very beginning.
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21 Times "Harry Potter" Was The Cleverest Book Series Ever