As mentioned in the comments, the second list (where bugs are missing) is where we get the initial command of numbers.
Since some of the animals ate bugs, it's fair to assume that a lot of edible bugs were in the Ark, for food. (There's even a Medrash that one of the birds went on a hunger strike until of the Noach's sons discovered that it only ate a certain worm found in rotten fruit.)
At the same time surely there were 2 privileged bugs of each type that were saved for posterity's sake - kept in their own cage/shelf or however they divided up the ark.
That said, the Chumash Torah Shleimah in footnote 211 - תורה שלמה in [ריא] in פרשת נח brings a Tanchuma Yashan (62) תנחומה ישן נח ס"ב which mentions the following:
Rabbi Akiva says (based on a דיוק in a פסוק) that everybody and
everything in the Ark ate the same food. This had to be the דבלה
(pumpkin? squash?) since both humans and animals consume it. (The
former cooked, the latter raw.). The Rabanan רבנן argue, saying that
each species had its own food.