It was hardly the sanguine end to the quarter that investors had hoped for—and a day that left many money managers feeling on edge as they head into the final few months of the year.

Central bankers who were thinking this year’s rise in inflation would wind up being a short-term phenomenon aren’t sure how long transitory pressures will persist. Strategists who had predicted another strong quarter of economic growth are cutting estimates because of supply-chain bottlenecks and the highly contagious Delta variant of Covid-19. Economic data have also been falling short of expectations.

Citigroup’s

Economic Surprise Index, which tracks how much U.S. reports have been exceeding or undershooting estimates, fell this month to its lowest level since June 2020.

The month proved a major setback for stocks, with all but one of the S&P 500’s 11 sectors finishing lower in September.

All told, the S&P 500 is still up 15% for the year and managed to squeeze out a sixth straight quarter of gains. The index is just a few percentage points away from its record close hit in early September.

“Sometimes the narrative is clean and easy,” said

Keith Lerner,

co-chief investment officer of Truist Advisory Services. But now, “I feel like you’re having to find opportunities in a market where not everything is moving together anymore.”

While Mr. Lerner is still betting on stocks rising over the long term, his firm has trimmed its exposure to emerging markets and focused heavily on the U.S., where he expects the economy to be most resilient, even as the global recovery slows.

One of the most vexing issues for investors and analysts over the past few months has been how quickly the market has churned through winners and losers.

Markets behaved relatively predictably in the first half of the year. Investors favored shares of economically sensitive companies such as banks, manufacturers and airlines and rebuffed relatively pricey technology stocks when it looked as though the rollout of Covid-19 vaccines would help supercharge the economy’s recovery.

This quarter, as the so-called reopening trade stalled, it became harder for investors to pick dominant trades. Technology stocks surged but then took the brunt of market selloffs in early September and this week—sending the S&P 500 Growth Index to its biggest monthly pullback since March 2020.

The bond market also caught many investors off guard. The yield on the 10-year U.S. Treasury note flitted about a narrow range for much of the quarter, only to stage a six-day rise above 1.50% between last week and Tuesday—its biggest such advance since June 2020, according to Dow Jones Market Data. The move came after the Federal Reserve indicated it was ready to begin reversing its pandemic stimulus programs as early as November and considering raising interest rates next year, given a jump in inflation.

“Even though there’s all this discussion about the market being resilient, the churn under the surface has shown more weakness,” said

Liz Ann Sonders,

chief investment strategist of Charles Schwab.

Ms. Sonders attributed the swift rotations taking place in the market to a bevy of investor worries.

“You have concerns about the virus, then you add on top of it concerns about the debt ceiling, some arguably more mixed economic data recently, [and] uncertainty about monetary policy,” she said. “I don’t know if we’ll get out of this mode anytime soon.”

Another issue weighing on investors’ minds: inflation.

So far this year, companies have been able to post robust profits despite rising costs for raw materials and labor. Earnings for S&P 500 companies have beaten analysts’ estimates by double-digit percentages since the second quarter of 2020, according to Morgan Stanley equity strategist

Michael Wilson.

That is compared with a median beat rate of 5% going back to 2008.

Yet with supply-chain disruptions and labor shortages persisting around the country, Mr. Wilson said it is hard to believe companies will be able to maintain that momentum.

Between June and September, 224 S&P 500 companies mentioned inflation on their second-quarter earnings calls, according to FactSet. That is the highest number since FactSet began tracking the data in 2010.

Historically, when a relatively high number of companies have mentioned inflation, profit margins have shrunk, Mr. Wilson said.

Investors are left grappling with one big question: How much of that has already been priced into markets?

“I’m a little concerned about 2022,” said

Karyn Cavanaugh,

chief investment officer of Carolinas Wealth Management. “When we don’t see the double-digit increases we’re used to for earnings, are the markets going to ask, ‘Hey, what have you done for me lately?’ ”

Ms. Cavanaugh has been advising clients to focus on “wide moat stocks”—companies with a strong record of delivering profits regardless of whether growth is slowing or accelerating because they maintain a competitive advantage over their peers.

Given so many potential issues remain unresolved, from debt negotiations and potential changes to the tax code in Washington to the pandemic, Ms. Cavanaugh said she expects the market’s path from here to be bumpy.

“We could be in for a bit of a grind,” she said.

Write to Akane Otani at akane.otani@wsj.com