Taking a cropped screenshot not working correctly

When I try to take a screenshot of a portion of my screen (CMD + SHFT+ 4) no matter where or what I'm trying to screenshot, the picture comes out as a screenshot of my desktop background for the portion of the screen I'm trying to grab. The screenshot bypasses everything currently on the screen and just takes a sectioned background photo, like nothing is even open in front of it. If I take a fullscreen screenshot (or record my screen), it will take a picture (or record) of everything accurately - all my current open windows. I know the simple answer is to just take fullscreen screenshots, but what's the point of having an option to take a screenshot of specific areas and it not doing that very thing? Was there a setting I can toggle on and off that I may have accidentally clicked? Thank you!