All of my applications are tracked in Application Usage except for one.
Chronories uses Spotlight to identify the applications on your system. You can set up Chronories to ignore applications. Please check these settings in Chronories' "Preferences - Categories - Applications Used".
If more than one application (or even all) are missing, chances are Spotlight is set up to ignore the entire Applications folder. Please open System Preferences then and select Spotlight - Privacy. If your Applications folder is listed there, please select and then remove it from the Privacy list by clicking the minus button.
More information about Chronories is available in the User Guide. You can find it in Chronories' Help Menu or for download here.