FIX that worked for me:

1. Go to the set up of your particular Expense GL Account for the transactions that you are missing.

2. Edit them and change the "Tax form section" to Other Business Expenses.

NOTE: If there the GL account is a subcategory to another GL account, you will need to change the parent account as well.

This is an issue with the GL account set up and the Tax form section, QBO doesn't read particular accounts for the Project expenses. For example, payroll expenses (if you have a 3rd party processor) will not show up. I think because QBO has their own timetracking and payroll software and it is meant to integrate with that.