Audit Bar Lines with a pick up note (anacrusis)
If you want to use Tools: Audit, Audit Bar Lines to check your bar alignment and have a pick up note, you need to isolate the pick up note before doing the audit. You can isolate the note by placing a double bar line or section close (Insert: Bar Line Decorated) after the note instead of a single bar line. Then run the audit. When the audit is complete, replace the double bar line with a regular bar line.