In "Birches" by Robert Frost, the central ambiguity is not in nature itself but in human understanding of nature. In a sense, the poem seems informed by Analogy of Religion, Natural and Revealed by Bishop Joseph Butler, a work that has informed much mainline anglophone Protestant thinking about how we understand the world. Butler argues that just as we see ambiguities and things we cannot explain in nature, so too religious truths can often seem ambiguous and mysterious. This is due not to religion or science being false, but to the necessary incompleteness of inductive knowledge.
The first ambiguity Frost addresses is the cause of the bent birches. He knows by induction that boys can bend birches by swinging on them and first uses this information to extrapolate that the bent birches he sees were bent by repeated use by a boy. Next, he realizes that in fact boys' swinging would not cause birches to stay bent. He notes:
But I was going to say when Truth broke in
With all her matter-of-fact about the ice-storm
I should prefer to have some boy bend them ...
In these lines, he presents an understanding of how we think about causation. We tend to personify causes and think about humans (and human intention and design) as explaining natural phenomena, whether literally or by analogy, but this is actually an artifact of our own desire for explanation in our own terms. What makes nature ambiguous is that it does not function in human terms and thus we cannot fully understand it. Instead nature exists at the intersection of Heaven (a mysterious divine will) and earth (the nature we perceive around us) and acts as an intermediary between the divine and human, something symbolized by the birch tree which lets the poet (metaphorically) repeatedly reach up to heaven and return to earth in the lines:
And climb black branches up a snow-white trunk
Toward heaven, till the tree could bear no more,
But dipped its top and set me down again.