Because animals have such a limited intellectual capacity, how can they be held culpable for anything that warrants a punishment as severe as the mabul?
The simple answer is because even the animals had descended into a state of absolute depravity and immorality and therefore also warranted destruction.
The Torah tells us in Bereishis 6:12:
וַיַּ֧רְא אֱלֹהִ֛ים אֶת־הָאָ֖רֶץ וְהִנֵּ֣ה נִשְׁחָ֑תָה כִּֽי־הִשְׁחִ֧ית כָּל־בָּשָׂ֛ר אֶת־דַּרְכּ֖וֹ עַל־הָאָֽרֶץ
When G-d saw how corrupt the earth was, for all flesh had corrupted its ways on earth,
and then continues (Bereishis 6:13):
וַיֹּ֨אמֶר אֱלֹקים לְנֹ֗חַ קֵ֤ץ כָּל־בָּשָׂר֙ בָּ֣א לְפָנַ֔י כִּֽי־מָלְאָ֥ה הָאָ֛רֶץ חָמָ֖ס מִפְּנֵיהֶ֑ם וְהִנְנִ֥י מַשְׁחִיתָ֖ם אֶת־הָאָֽרֶץ
G-d said to Noach, “I have decided to put an end to all flesh, for the earth is filled with lawlessness because of them: I am about to destroy them with the earth.
The midrash in Bereishis Rabbah 28:8 writes:
רַבִּי עֲזַרְיָה בְּשֵׁם רַבִּי יְהוּדָה בַּר סִימוֹן אָמַר, הַכֹּל קִלְקְלוּ מַעֲשֵׂיהֶן בְּדוֹר הַמַּבּוּל, הַכֶּלֶב הָיָה הוֹלֵךְ אֵצֶל הַזְּאֵב, וְהַתַּרְנְגוֹל הָיָה מְהַלֵּךְ אֵצֶל הַטַּוָּס, הֲדָא הוּא דִכְתִיב (בראשית ו, יב): כִּי הִשְׁחִית כָּל בָּשָׂר, הִשְׁחִית כָּל אָדָם אֵין כְּתִיב, אֶלָּא כִּי הִשְׁחִית כָּל בָּשָׂר.
Rabbi Azariah in the name of Rabbi yehuda the son of Simon said, everyone's actions became corrupted in the generation of the flood. The dog would mate with the wolf, the rooster would mate with the peacock, thus it writes in Bereishis 6:12 - "For all flesh had corrupted" - it doesn't write "all humans" but rather "all flesh corrupted".