How do prevent TextWrangler save alert (This file appears to have been modified) on Mac?

Whenever I save a file in TextWrangler, I keep getting a popup alert with the text:

"The file at sample.sh may have been changed on disk by another application. If so, saving this document may cause data loss. Are you sure you wish to proceed?"

This is the popup itself*:

_{*Image taken on macOS 10.13.6.}

What is causing this and how can I prevent it from happening?

Here is a workaround: Turn off "Automatically refresh documents as they change on disk" in Preferences->Application.