Is it permissible to understand the Quranic verses that include scientific facts in accordance with what modern science has proven, such as the word "nutfa"?

The phrasing of the question is unclear. "Nutfa" (نطفة) means a small amount of water, and in the Quran, it refers to the man's water (sperm). This meaning does not change with scientific advancement. It is not permissible to interpret "nutfa" in a way that contradicts this meaning. As for introducing new interpretations of Quranic verses based on contemporary scientific facts, if these interpretations imply that the meanings of the verses were hidden from the early Muslims (Salaf) and that they were mistaken, then this is unacceptable. However, if the new interpretation is an inference of additional meanings that do not invalidate the interpretations of predecessors, nor claim that the meaning was hidden from them, then there is no objection, provided certain conditions are met: that the interpretation offered is sound, that the verse can bear it, that it does not invalidate the interpretations of the Salaf, and that the meaning of the verse is not restricted solely to it.