These are the settings I have in place. I have tried setting the alerts for a single document and entire libraries. The users still receive multiple emails instead of a daily summary. I am unsure how to stop the multiple emails and only alert users with a daily summary. Any suggestions are welcome.
I tested with the same settings, the Email do only get sent once a day. No multiple emails are received. Have you test with alerts on other lists/libraries? You may try to recreate a new one and test again.
And just a notice, the alert does not work at file level, it works at list/library level. Which means you cannot make it only work on a specific file. All files in the library will trigger the alert to send email.
First, You can create an alert for a specific document to receive an email when the document changed.
Regarding, your issue. it's actually strange behavior, so I suggest to check all alerts that have been created for this library/list as mentioned at SharePoint 2016 Get All User Alerts By List Name, and make sure that there is no alert that set to trigger immediately.