It’s normal for an incoming President to redecorate the Oval Office. There a couple of decorations which have become traditional, such as the painting called "The Avenue in the Rain" (which Trump removed, and which Biden has brought back), but it’s up to whoever holds the Office.
U.S President Joe Biden has decorated his new office with busts of civil rights and labor leaders, nods to other presidents who faced great crises, and side-by-side portraits of American founders who famously disagreed.
The Oval Office is the formal working space for the president, and most choose new drapery, furniture and carpets when they enter, as well as art and artifacts from the White House collection, museums and collectors. A portrait of former President Andrew Jackson, who espoused a populist political style that has sometimes been compared with that of Trump, is gone.
The "military flags" in question are the two to Trump’s left, flanking a portrait of Andrew Jackson. While it’s not unheard of for Presidents to display flags representing branches of the military, they’re not traditional. Most modern Presidents have only had the two directly behind the Resolute Desk, which are the flag of the United States and one bearing the seal of the office of the President. It’s weird that some people are trying to make a big deal out of something that happens every time a new President takes office.