How did the polar bears and penguins reach Noah's ark?
That’s a good question. The answer depends on what actually happened in history.
The Catholic Church does not prohibit interpretations of Genesis 6-8 that include a worldwide flood, but neither does the Church require there to be a worldwide flood in all interpretations of these passages. Instead, according to Pope Pius XII, “in simple and metaphorical language adapted to the mentality of a people but little cultured,” the first eleven chapters of Genesis “both state the principal truths which are fundamental for our salvation, and also give a popular description of the origin of the human race and the chosen people” (Humani Generis 38).
Consequently, the flood could be understood as impacting the entire world, or possibly a large region of the world. If it did impact the entire world, animals in distant regions would likely have been miraculously transported to the ark.
On the other hand, if the flood was more regional, a view which has gained increasing traction in recent centuries because of scientific findings, then all the animals of the world would not have been destroyed, and thus polar bears and penguins would not have been affected.
For more on this topic, please see this article in Catholic Answer Magazine Online.