Hi Greg,
In the context of loading a topology to a fabric, the Exceptions are reserved for lines that are to be imported as non-boundary lines, or non-road frontage lines, or for lines that do not form a required boundary of a parcel and should be ignored.
For example: by definition, a connection line will break the rule "Must be Covered by Boundary of"
However, this should not prevent you from importing connection lines, and so you can mark these lines as exceptions, place a field on the source data called "Category" and then populate these lines with the value '3' so that they will then be imported as connection lines.
If they are to be ignored then you'd mark them as exceptions and not give them a category value at all. There are some limits to what should be marked as an exception. For example, if an exception is set on a line that would be used as a boundary if it were not for its topology error, then the results of the import may result in the type of problems that you are reporting.
-Tim