This is normal Lightroom behavior and usually depends on where you are in the app.

In the Library module, flags, star ratings, and color labels are applied to all selected photos. In Develop, Book, and Print, they apply only to the active photo.

If this happened in Library/Survey view, the likely cause is Auto Sync being enabled. Turning off Auto Sync should stop ratings/flags from being applied across the whole selection.

If you want to be sure only one image is affected in Library, deselect the others first with Ctrl+D (Cmd+D on Mac), which is Select None, then click the single photo you want to rate or flag.

So: there isn’t a single preference that changes this globally; it’s mainly controlled by the current module/view and whether Auto Sync is on.