Reporting limitations on multi-select custom fields
When you create a multi-select custom field such as a Checkbox field, you can attach the form to an object, and create a report on that object type. However; when you want to exclude results that have one of the options selected, the report will display any objects that have that option and any other option selected.
Why a filter on multi-select custom fields doesn't work
Workfront's filtering system is very specific.
For example: If you have a field with 3 options, and select 2 of the 3 options (A+B, but not C) on an object, you can create a report with a filter with a qualifier of not equals for options A + B, and it will only filter out projects that have both A+B, but not only A, and not only B selected. If you create a filter with a qualifier for not equals for option A, it will only filter out objects with only A selected, but if A + B are selected, those objects will still appear.