I am currently running Manjaro KDE on Linux 5.8. Whenever I try to take a screenshot with Spectacle, it cannot capture any open applications or windows. Instead, it shows only the desktop. Does anyone know how to fix this?

From the drop down menu here are your options.

Capture mode

This will further change how the image will look when it's finally saved. Options here include;

Full Screen (All Monitors): Everything is captured

Current Screen: Everything on the current screen is captured

Active Window: Active Window contents

Window under cursor: Window contents below the cursor

Rectangular Region: Capture a rectangular region

You can use "Active Window: Active Window contents" to get the app you last clicked on or use "Rectangular Region: Capture a rectangular region" to select the window you want.