Here are two lines (台詞) from different animes.
女の子って、何でできてる？ (放浪息子)
でも、それ、じゃ赤ちゃんってどうしてできるんだろう (苺ましまろ)
I'm wondering why the verb できる (make) appears in the different tenses but it's expressing same action (they both means make in the lines above).
Shall I be aware of the difference between the verb tenses in the sentences above and how do I distinguish them (if the tenses expresses different meaning)?
Those questions are fundamentally different in meaning:
女の子って、何でできてる？
What is a girl made of?
What are the essential elements/components of a girl?赤ちゃんってどうしてできる？
Why do babies come to be?
How does a baby come into existence?
In the first sentence, the question is about already-grown teenager girls who were born many years ago. What the speaker has in mind is not a newborn but a female student, and the question has nothing to do with the process of pregnancy. できて(い)る is the natural choice because it's about the result of an event that happened many years ago. Note that this 何で means "with what", not "why". (放浪息子 is a story about a 女装男子. The phrase in question may be a reference to this.)
On the other hand, the second question is about pregnancy; the speaker is thinking about a newborn who appears (seemingly) from nowhere. Since it's directly about the process of できる itself, the present tense is the correct choice.
