These are from the Midnight Library series by Damien Graves.
"One was about this boy that stole an apple from his neighbors backyard and turned into a tree."
This is "An Apple a Day" from Voices (2007).
A summary from a review (spelling/style corrected, emphasis mine):
The last story, "An Apple a Day"...is about a young boy named Tim who is mad about his neighbor scaring his grandma after his neighbor accuses him of eating one of his apples. Tim tries to get him back by spelling out the word "bully" with his own apples in his backyard and eating one of the apples. Strange things start happening the next day when he starts coughing up apple seeds and growing leaves out of his ear. The book slowly turns Tim into a literal apple tree.
"...this girl's friends were throwing rocks at this old lady’s window and she hits and kills a cat, then she turns into a cat and gets killed."
This is "The Cat Lady", from the book of the same name (2007).
A blurb (emphasis mine):
Chloe never quite believed her friends' stories about the Cat Lady. But when a dare goes horribly wrong, she finds out that the truth is more terrifying than anyone had ever imagined...
"...each book had two or three plots."
From the same summary:
Plus, two more terrible tales...
"There was also a story about a girl who could hear phone calls and radio frequencies in her head."
This is "Voices" from the book of the same name (2007).
A summary from a review (grammar corrected, emphasis added):
The book is about a girl who is going through some problems with her family's health and such. Her mom ends up in the hospital and there's not exactly anything that she can do. She hears voices of people talking, listens into phone calls between people all the time, and this so-called power isn't something she can control.
boy turns into "tree" scary "apple" book and found this answer.