How do I get rid of a small grey box on my iMac screen?

If this is caused by omnifocus I would quit using that app. If you're really in need of it, delete the app and install it again to see if the issues persist. You can also contact the developer to see if this is a common issue in using omnifocus

Where is the grey square located? you can try and start the Mac in the safe mode to rule out that this is caused by a software issue

See this instructions on how to boot your Mac in the safe mode

Start up your Mac with Apple silicon in safe mode

1. On your Mac, choose Apple menu  > Shut Down.
2. Wait for your Mac to shut down completely. A Mac is completely shut down when the screen is black and any lights (including in the Touch Bar) are off.
3. Press and hold the power button on your Mac until “Loading startup options” appears.
4. Select a volume.
5. Press and hold the Shift key, then click Continue in Safe Mode.
6. The computer restarts automatically. When the login window appears, you should see “Safe Boot” in the menu bar.

Start up your Intel-based Mac in safe mode

1. Turn on or restart your Mac, then immediately press and hold the Shift key until you see the login window.
2. Log in to your Mac.
3. You might be asked to log in again.
4. On either the first or second login window, you should see “Safe Boot” in the menu bar.

Does it show up in a screenshot?