I assume that you're breaking down the Marketing Channel dimension's values by the Tracking Code dimension. And I further assume that your Tracking Code has been configured with the default "Week" Expiry.
In that case, what you're observing is reasonable. Consider this scenario:
Monday: Enter your site with the tracking code "foo".
Wednesday: Enter your site without any tracking code.
Let's say you have a Marketing Channel Processing Rule that states that if Query String Parameter contains "foo", then the Marketing Channel is "Display".
Result:
You have 2 Total Entries for Marketing Channel: 1 for "Display" (from Monday's entry), 1 for "Direct" (from Wednesday's entry).
You also have 2 Total Entries for Tracking Code, and both Entries are for "foo". The reason is that AA persists your Tracking Code value for up to a week (7 days). Wednesday is just 2 days after Monday, so Wednesday's entry gets attributed to "foo" too.
So, when you break down Marketing Channel by Tracking Code, your Entry from Wednesday gets reported with "Direct" Marketing Channel and "foo" Tracking Code.
To prevent such reporting discrepancies: always breakdown Marketing Channel by Marketing Channel Detail instead. That ensures that both dimensions are reported with the same persistence.