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Apple's forecast-beating earnings Tuesday left some analysts worried it's selling too many of its lower cost iPhone SE model and needs to diversify its current portfolio of smartphones.

"Margins went down, they sold a lot more iPhones SE than they had expected to, and Apple needs to be very careful of that," Moor Insights & Strategy's Patrick Moorhead told CNBC Wednesday.

The technology giant reported earnings of $1.42 per share on revenues of $42.4 billion. Despite beating estimates, that was down against the comparable year-ago figure of $1.85 per share on $49.61 billion in revenue. It shipped 40.4 million iPhones in the third fiscal quarter, also above estimates.

'Apple needs to do something else'

Chief Executive Tim Cook said in a conference call that the strategy of launching the lower cost iPhone SE was working and attracting customers to Apple's ecosystem. However, some are wary of this bright spot in the report and suggest a popular cheaper model means tighter margins and less consumers buying the more expensive products.

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"(They were) very good numbers. However, they show that Apple needs to do something else," Francisco Jeronimo, research director for European mobile devices at analysis firm IDC, told CNBC Wednesday.

"The price point shows that they need to do something else in terms of the entire (iPhone) portfolio because the market is not growing anymore. And if it's not growing, or even if it's only growing in emerging markets where most consumers cannot afford the top of the range, they need to move towards lower price ranges and that's basically what the iPhone SE did this quarter to Apple," he added.

"They sold more iPhones SE than iPhone 6 or 6s which is a very strong indicator that they need to do something in that space."

Moorhead believes that if Apple releases a next-generation iPhone 7 this year then that could lead to a much "better balance" for profit margins at the Cupertino, California-based company.

"They need to watch it very closely as the SE is a drop," he said.

'Bear case is less compelling'

David Paul Morris | Bloomberg | Getty Images

There's speculation that this new top-of-the-range model could come as early as September. Evan Blass, a prominent Apple watcher with an accurate track record of predicting the tech giant's releases, posted a tweet early Saturday saying the latest iPhone iteration would be released the week of September 12. Apple has given no overt indication that it's planning an event.

Wall Street had a more optimistic take on Apple's earning Tuesday, with a slew of price upgrades overnight. JPMorgan raised its price target on Apple to $107 from $105, according to Reuters. Macquarie upped its target to $115 from $112 and Maxim Group raised its projection to $173 from $168. There was also an upgrade from BTIG.

Morgan Stanley's equity analyst Katy Huberty isn't as concerned on overall margins and believes that Apple appears to be fairly supply-constrained on the iPhone SE handset. In a new research note overnight, she said that these new results and guidance would push the "margin debate to the back burner."

"June quarter gross margin came in at the high end of the guidance range despite higher than expected channel inventory reductions as COGS (cost of goods sold) were better than expected due to component cost declines and better product quality," she said.

"While we fully expect investors to question the impact of a higher iPhone 7 bill of materials like in past cycles, the gross margin bear case is less compelling as Apple just gave stable gross margin guidance."

—CNBC's Javier E. David and Anita Balakrishnan contributed to this article.