The Litecoin Developers are aware of a regression introduced in Litecoin Core v0.21.3. A certain number of users may see the error message "Prune mode is incompatible with -blockfilterindex." on startup.
Locate the Litecoin Data Directory. By default this is located at:
macOS: ~/Library/Application Support/Litecoin
Linux: ~/.litecoin
Windows: %APPDATA%\Litecoin