Why is the Missouri River considered as a tributary of the Mississippi River, despite the Missouri being longer?

There is no universally agreed upon definition such that any stream's source can be systematically determined. The United States Geological Survey (USGS) states that a river's "length may be considered to be the distance from the mouth to the most distant headwater source (irrespective of stream name) or from the mouth to the headwaters of the stream commonly identified as the source stream". Thus, for example, the USGS considered the Missouri River a tributary of the Mississippi River, despite the Missouri being longer.

https://en.wikipedia.org/wiki/Source_(river_or_stream)

Blame it on Lewis and Clark (further to the above answer.)

"The Missouri in name officially begins at Missouri Headwaters State Park at 4,045 feet (1,233 m) in Montana at the confluence of the Jefferson River and Madison River. The Gallatin River joins the river about 0.6 of a mile downstream as it flows northeast. The Jefferson River originates in southwest Montana near the Continental Divide. The Madison and Gallatin Rivers flow out of northwest Wyoming to meet the Jefferson River.

Meriwether Lewis in his journal entry on July 28, 1805 wrote:

Both Capt. C. and myself corresponded in opinon with rispect(sic) to the impropriety of calling either of these [three] streams the Missouri and accordingly agreed to name them after the President of the United States and the Secretaries of the Treasury and state.

The Lewis and Clark decision not to call the Jefferson the Missouri has spurred debate over what is the longest river in North America since the Missouri and Mississippi are nearly identical in length. With the Jefferson the Missouri would be the longest river."

https://en.wikipedia.org/wiki/Missouri_River