Windows says "Windows protected your PC"
That's SmartScreen. The app is only flagged because it isn't signed. Click More info, then Run anyway. Windows remembers your choice.
macOS won't open it
Gatekeeper blocks unsigned apps the first time. Try to open it once and dismiss the warning, then go to System Settings → Privacy & Security, scroll down to Security and click Open Anyway. Open it again and confirm. You only need to do this once, for the app and for the command line alike.
Double-clicking manga-downloader.exe just flashes a window
That's the command line tool, which runs from a terminal. Use the PowerShell one-liner and run it from there, or get the desktop app if you'd rather click.
The newest chapter downloads empty or is missing
Many sites keep their latest chapters behind a paywall, and the page often looks normal. Try a slightly older chapter to confirm that the site works.
Old chapters are missing, or a warning says the range starts before the first chapter
Sites often delete old chapters. manga downloader can only download chapters that the site still lists.
A browser window pops up
That's expected for sites tagged browser in the list. The window opens when the site shows a Cloudflare challenge. Checkboxes are clicked automatically, but some challenges need you to click them yourself.
Pages don't show up on my e-reader
The site probably serves WebP images. Download the chapters again with --convert-images avif,webp.
My site isn't supported
Try it anyway: sites built on the same platforms as listed ones often work. If it doesn't, open an issue or send a pull request.