A belated "Welcome to the forum!" Diabolik.
If you're using Monarch Pro, then this can be fairly straightforward. If that's not the case, well, then there's some work ahead.
I'll assume that you've got Pro.
First, open a Monarch project that loads your "[B]STUFF THAT IS SUPPOSED TO BE IN THE DATA FILES[/B]". Maybe that's a report, perhaps it's an Excel list or even a .csv file.
Now in the Table window create an external lookup which references the "[B]STUFF THAT ACTUALLY CAME DOWN FOR THE DAY[/B]" file, using the common field, say "Fruit". Import the Fruit field from the external file as FruitCheck.
Monarch will give you
Apples Apples[/code]when Apples exists in both files, and
Apples (Null)[/code]when Apples does not exist in the external file (the daily file).
That said, the appearance of the value of (Null) is controlled in the Options->View menu so it might be blank, (Null), or some other value of your choice.
Now you can build a filter to isolate the items that don't exist in the daily file by using this expression:
PS. Do donuts qualify as fruit? Maybe apple fritters?