Last Tuesday, Buzz Bissinger hopped the Amtrak train to Philadelphia from New York, where he had done a bit of publicity for “After Friday Night Lights,” a 12,000-word e-book that had been performing nicely since its release. But when he opened his laptop to check his ranking on Amazon, he found the book was no longer for sale there.


“I was stunned,” he said in a phone interview on Friday. “I thought it was some kind of technical difficulty.” (I had noticed a lot of people on Twitter shared his confusion.)


Depending on how you define it, he was right. Mr. Bissinger, the best-selling author of multiple books, including “Friday Night Lights,” had written the e-book as a postscript for the popular book about high school football in Texas. “After Friday Night Lights” traces his relationship with Boobie Miles, a running back whose football career was derailed by an injury and who has been on a hard road ever since.


Mr. Bissinger wrote the e-book for Byliner.com, one of a number of fledgling companies trying to make a go of it by publishing long-form works — not as long as a traditional book, but longer than most magazine articles — for digital readers. Mr. Bissinger thought the e-book, priced at $2.99, would be a great way to pay tribute to the relationship while also helping Mr. Miles, by giving him a third of the proceeds.


But the plan hit a pothole after Apple, which had been looking to get into shorter works in a digital format, decided to include e-books in a promotion that it does with Starbucks. It selected Mr. Bissinger’s digital sequel as a Pick of the Week, giving customers a code they could redeem online for the book. (Mr. Bissinger said he still received a royalty of $1.50 for each copy sold.)


Amazon interpreted the promotion as a price drop and lowered its price for “After Friday Night Lights” to exactly zero. Byliner withdrew the book from Amazon’s shelves, saying it did so to “protect our authors’ interest.”


Mr. Bissinger, who has built a franchise on journalistic excellence and rhetorical intemperance — see his Twitter account — managed to choose his words carefully when talking about how his e-book ended up as a bug on the windshield of Amazon’s relentlessness on pricing.


That may have a little something to do with the fact that he has a great big book, “Father’s Day,” being released by Houghton Mifflin Harcourt in just two weeks. It would be a bad time to stick his finger in the eye of a company that sells more books — including his — than any other company in the world.


“It’s a shame that the e-book was not on sale at Amazon,” he said. “Amazon is a crucial outlet for any author, and when you lose them, it’s terrifying. It’s a killer for ‘After Friday Night Lights’ because it was just gaining momentum and books have a very small window of opportunity.”


In a statement, Byliner said the company had no choice in withdrawing the book.


“While we greatly value Amazon as a partner in this new category, we need to protect our authors’ interests,” the statement said. “As such, we had to remove the title from Amazon until May 1. We’re disappointed that Amazon customers won’t have access to this wonderful story, but we’re pleased that readers still have other options to purchase and enjoy Buzz’s powerful sequel.”


I reached Mark Bryant, one of the founders of Byliner and its editorial director, who was also careful when talking about Amazon’s role in the episode.


“We were very surprised,” he said. “Amazon has been a terrific partner. I don’t have any reason to think that they won’t be in the future.”


Mr. Bryant, who formerly edited a sports magazine for The New York Times, said that Amazon’s “price bot” had picked up the fact that the book was being given away as part of a weeklong promotion and responded by dropping its price to zero. (In an e-mail later, Mr. Bryant said that when the company told Amazon about the promotion, before it began, Byliner was warned the price might drop to zero. But, he said, “we hoped that wouldn’t happen.” It did.)


A spokeswoman for Amazon said that whether the book went back on sale at its regular price when the promotion ended was up to Byliner, not Amazon. “We expect and hope to be able to sell the single again next week,” she said. Apple declined to comment on decisions made by another company.


Founded in 2011, Byliner is a digital publishing company that features fiction and nonfiction at lengths from 5,000 words to 30,000 words. The company commissions works and then splits any royalties down the middle with the authors.


The company has had some success. One of its books, “Lifeboat No. 8,” was No. 1 on the New York Times e-books best-seller list, and “After Friday Night Lights” hit No. 19 on the list in its first week in circulation. Given that Amazon is the biggest seller of digital books by a wide margin, it probably won’t be on the list next week.


Amazon was a big beneficiary of the Justice Department’s recent decision to pursue price-fixing charges against Apple and book publishers, which had been fighting to gain control of e-book pricing and were working with Apple to push back against Amazon’s deep discounts. Mr. Bissinger now finds himself caught between Amazon and Apple, a situation that pretty much defines a rock and a hard place.


With the business performance of Amazon, it’s hard to suggest that the company does not know what it is doing, even when it “sells” a book at a price of zero. Last week, Amazon announced that it had blown away analysts’ expectations, with $13.8 billion in revenue for the first three months of the year. Its stock went up 13 percent.


Like Wal-Mart, Amazon is big enough to set prices in certain categories. Suppliers are left to scramble to meet those objectives or pass up the opportunity to work with the largest retailers in the world. Amazon’s might when it comes to pricing will only grow as the impact of the Justice Department’s lawsuit begins to emerge. But sometimes the company’s tactical aggression lands hard on the people who supply it.


Mr. Miles not only received a third of the commission for “After Friday Night Lights,” but also was sharing royalties with Mr. Bissinger as well.


“It’s too bad, because Boobie needs the money,” Mr. Bissinger said. “Hell, I need the money. Authors need everyone — Amazon, Apple, Barnes & Noble, Byliner — to make a go of it and to continue to do what we do.”