The San Francisco 49ers have already dealt with their fair share of issues this season. 

The defending NFC champions have seen multiple key players miss time due to injury, with even more uncertainty still surrounding All-Pro running back Christian McCaffrey. The injury-riddled Niners have dropped two consecutive games, but they are hoping to get back on the winning track when they return to the friendly confines of Levi's Stadium this Sunday.

Tempers flared this week, as the 49ers were going through preparations for their matchup with the New England Patriots. At one point during a recent practice, coach Kyle Shanahan told star wide receiver Brandon Aiyuk that his shorts were not the right color.

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Brandon Aiyuk talks to Kyle Shanahan

Brandon Aiyuk, #11, and Head Coach Kyle Shanahan of the San Francisco 49ers on the field before the game against the Seattle Seahawks at Lumen Field on December 15, 2022, in Seattle, Washington. (Michael Zagaris/San Francisco 49ers/Getty Images)

A video surfaced on social media showing the exchange between Shanahan and Aiyuk. The wide out was initially wearing red shorts. Other 49ers players appeared to be wearing black shorts during practice on Friday. 

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Moments after what appeared to be an animated conversation, Aiyuk removed his red gloves, cleats and red shorts. He then made a kicking motion while the piece of clothing was on the grass. He then picked up a pair of black shorts and put them on.

Shanahan was later asked about Aiyuk's attire. "Yeah, he did. Good question," Shanahan responded when asked whether the receiver had taken the practice field in the wrong shorts.

Shanahan dismissed the idea that Aiyuk would face further punishment for his actions. "No," the eight-year Niners coach said with a noticeable smirk. "I wish I could wear different shorts."

Brandon Aiyuk introduced before a game

Sept. 9, 2024; Santa Clara, California, USA; San Francisco 49ers wide receiver Brandon Aiyuk (11) is introduced to the crowd before the game against the New York Jets at Levi's Stadium.  (Darren Yamashita-Imagn Images)

Aiyuk signed a four-year contract extension worth up to $120 million last month, which marked the end of a rollercoaster offseason.

Multiple reports surfaced during the offseason stating a tentative agreement was in place to send Aiyuk to the Steelers via a trade. The extension with San Francisco came around one week before the 2024 regular season kicked off. 

Kyle Shanahan sidelines

San Francisco 49ers head coach Kyle Shanahan walks on the field before an NFL football game against the Minnesota Vikings, Sunday, Sept. 15, 2024, in Minneapolis.  (AP Photo/Abbie Parr)

Aiyuk enters Week 4 with 119 receiving yards. He has yet to score a touchdown. The All-Pro finished the 2023 campaign with a career-best 1,342 receiving yards.

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Jauan Jennings is the 49ers' leading receiver through the first three games. The fourth-year receiver has racked up 276 yards over the three-game span.

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