Here is the same story from an Indian newspaper:
https://www.thehindu.com/news/national/india-protests-us-nav...
A propaganda outlet seizing on the opportunity to focus on a disagreement between allies that it's antagonistic with is unsurprising. Just because The Hindu and the SCMP both reported on the incident does not itself vindicate the SCMP or it's reporting. Note the difference in reporting between the SCMP and The Hindu (Indian) with regard to the detail spent on the Exclusive Economic Zone, Domestic Waters, counterclaims from the US, etc.
EEZ =/= Internationally Recognized Territorial Waters. This was not a violation of Sovereign Territory. The real story here (if there is one at all) is the US not giving India a heads up ahead of time (which it's not required to do, but it would be a friendly gesture among allies). Meanwhile the SCMP makes it sound like the USN violated sovereign territory, and is capitalizing and small political spat between friends to justify it's own complaints against the US (and others) not recognizing the CCP's territorial overreach
Since the change of ownership in 2016, it has been alleged to be on a mission to promote China's soft power abroad.[9] According to critics, it is moving away from independent journalism and pioneering a new form of "propaganda".[9]
https://en.wikipedia.org/wiki/South_China_Morning_Post
There's a lot more in the article on bias at that organization. Bottom line: this publication carries propaganda, and the Chinese government has strong incentive to drive a wedge between India and the U.S.
Arguably, this works equally well ot better if you reverse it to “about India complaining about a foreign navy transiting through their EEZ waters” and retain the rest of thr post as is.