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Qur'an 16:66 states:
And indeed, for you in grazing livestock is a lesson. We give you drink from what is in their bellies - between excretion and blood - pure milk, palatable to drinkers.
Scientifically speaking, I believe the cow does not produce the milk in its stomach, unless I'm wrong.
Belly does not mean stomach. And especially the arabic word use 'Batn' does not mean the scientific stomach:
i.e. it includes the udder
You can't use the modern day scientific definition of a word and apply it to the Quran. Imagine if the Quran was revealed in English and it used the word 'stomach'. Would you now assume that the Quran means the exact scientific organ that was named 'stomach'. No, that is ridiculous. It means the definition of the stomach at the time of revelation. 'Stomach' for centuries meant exactly what 'Batn' means namely the whole area including all the organs.
No, the verse does not discuss an organ; it discusses a process.
In classical exegeses of the Qur'an, you will find that the verse does not discuss the place at which milk leaves the body of animals. Ibn 'Ashūr, in his tafsīr, explains that literary devices used in this verse as well as its intended meaning:
وموقع من بين فرث ودم موقع الصفة ل لبنا، قدمت عليه للاهتمام بها لأنها موضع العبرة، فكان لها مزيد اهتمام، وقد صارت بالتقديم حالا
NOTE. My own translation, so treat with care.
And the position of intermediacy of pomace and blood is descriptive of the milk, introduced earlier to draw attention to its intended meaning, which gives it more attention as when introduced earlier [in the sentence], it becomes a status [gramatically].
Ibn 'Ashūr further elaborated that milk was put as the object (maf'ūl, Arabic: مفعول) of "give you to drink" (Arabic: نسقيكم) to signify that the verse is not referring to a place of serving (i.e., udders), rather; to an outcome product based on two agents: cud and blood. The milk goes from "within" (butūnih, Arabic: بطونه) as excretion or blood would, but it is tasty and easy to swallow.
Note that the word used is butūnih, which is in a masculine form, whereas the word an'ām (animals specified in the verse) is in a feminine form, which would lend itself to using the word butūniha (feminine) rather butūnih (masculine). Linguistically, the origin of the word is batan (Arabic: بطن) has multiple meanings as is the case with most words of the Arabic language:
The word batan (Arabic: بطن) in its root format refers to what is below and concealed, with its antonym being dhahar (Arabic: ظهر) referring to what is above and apparent:
وَلَا تَقْرَبُوا الْفَوَاحِشَ مَا ظَهَرَ مِنْهَا وَمَا بَطَنَ
And do not approach immoralities — what is apparent of them and what is concealed.
This is often used as a literary device in the Arabic language and has often caused confusion when translating such words as batan can also mean belly (or bowel) and dhahar can also mean back.
Such usage was discussed by Sami Wadī' in his book At-Tafsīr al-Bayāni, pp. 133-134 that is dedicated to the understanding of the linguistic and theological meaning of the words used in this chapter (not specifically verse 66, but it is covered too). He explained that the word farath (Arabic: فرث) referred to pomace. In the case of this verse, it is referring to the point of the process starting with the cud in fermented ingestion to the point where nutrients are transported through blood, and how milk — which neither resembles pomace nor blood — is formed. He, too, did not see that the verse referred to an organ, but to a process.
As @TheZ said, the word (batn بطن and its plural butoon بطون) which is mentioned in the Ayah is more general than stomach ... It includes the abdomen (or the internal origins) ... and one example to think about is that the word Internal medicine ... it is translated to tebb batny طب باطنى
