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Tesla’s surprise profit—news that triggered a two-day gain of almost 29% for the stock this month—wasn’t as good as it looked, a securities filing indicates.

The electric-vehicle company (ticker: TSLA) filed its full third-quarter financial report with the Securities and Exchange Commission on Tuesday morning, using a so-called form 10-Q. “Q” filings contain more detail than companies usually report in their earnings news releases.

Tesla’s latest 10-Q contains data on warranty expenses that appears to have upset investors. The stock was down 2.6% in afternoon trading, while the Dow Jones Industrial Average was a touch higher. One analyst downgraded the stock.

All car companies record warranty expenses on an “accrual” basis. That means they recognize an expense—reducing reported earnings—before repairs covered by warranties actually occur. Cars break sometimes and everyone knows it. Estimating warranty costs ahead of time gives investors a better sense of the underlying profitability of car operations.

Tesla recognized $153 million in warranty expense for the second quarter of 2019. It sold $5.2 billion worth of cars, so warranty costs represented about 2.9% of that revenue, but the ratio fell to about 2.7% for the third quarter.

Is this a big deal? If the warranty-expense rate hadn’t changed, Tesla’s pretax income would have been about $12 million lower. Tesla reported a pretax profit of $176 million during the second quarter.

Tesla also reduced its overall accrual for previously existing warranties. It doesn’t think it will have to provide as many warranty repairs as it once believed. That is another change that was reflected in the third-quarter income statement, accounting expert Bob Willens tells Barron’s.

It added another $37 million in third-quarter pretax income, bringing the total warranty-related boost to almost $50 million. It’s a substantial figure, compared with the $176 million profit Tesla reported.

Still, investors expected Tesla to lose money in the third quarter. The warranty changes aren’t enough to account for the entire unexpected profit.

It’s impossible to know exactly why the warranty rate and accrual changed. Tesla wasn’t immediately available to comment. But generally speaking, factors such as the mix of goods sold, quality statistics, and actual warranty expenses inform cost estimates.

Tesla, for instance, only paid out $59 million in warranty cash during the third quarter. The outflow was much smaller than the expense recognized. Warranty expenses are often small early in a car’s life. Tesla deliveries are growing so it is putting more new cars into its existing fleet, reducing the average age of the vehicles.

Nevertheless, the warranty issue was enough for Roth Capital to downgrade the stock at midday. Analyst Craig Irwin cut his rating from the equivalent of Hold to Sell. He left his target price unchanged at $249 a share.

The changing assumptions on warranties boosted margins. “We see margins as unsustainable,” wrote Irwin in a research report.

Investors want to see more consistent profits and cash flow. The third- quarter results qualified as a big win for bulls. Tuesday’s news is fodder for bears. Tesla will remain a controversial stock.

Write to Al Root at allen.root@dowjones.com