Today, I encountered a complicated sentence: "When you don't know the biology of a species, to unjustifiably claim it suffers abuse, is stressed or depressed, is to make one of man's most common mistakes, which is to humanize animal behavior." When I read this sentence for the first time, I was not able to understand what ithis meant.

The "it" [in my correction, haha] refers to the sentence.

After wonderingthinking about it for a while, I noticrealized that "it in the sentence was" referrings to "a species," and I was able to fully understand this sentence.

I agree with the previous suggestion with one improvement--don't forget that a comma goes before a coordinating conjunction that connects two independent clauses.

After wondering for a while, I noticed that "it in the sentence" was referring to "a species" and I was able to fully understand this sentence.

After wondering for a while, I noticed that it in the sentence was referring to a species and I [was able to] fully understand ithis sentence.

惜しかったです！the sentenceもう書いたので、this sentenceはいらないです。