John knows who went to the store
is said to have the embedded question, "who went to the store". Likewise, you could have "John knows where the store is", "John knows what is at the store", "John knows whether there is a store down the street", and so forth. These kinds of claims are often known as knowledge-wh propositions. The object, e.g., "who went to the store" is sometimes known as the wh-complement.
The fundamental problem with all of this is that the wh-complement in knowledge-wh propositions is not a question at all. The "who went to the store" in "John knows who went to the store" is not a question; it does not mean "Who went to the store?" but is just a description for the person or persons of whom it can be said that they went to the store. The claim is not that John knows the question "Who went to the store?" John knows who it is that went to the store.
Contrast this with cases involving a real embedded question:
John wondered who the man was.
John wondered, "Who was that man?"
These give us genuine interrogative expressions (the first indirectly, the second directly). The examples noted above do not, and therefore have nothing whatsoever to do with questions and how they work.
The usual way of handling this is to treat the wh-complement as a question, but one indicating the set of answers to the question; but as questions are not their answers, or any set of them, this is simply worthless.
To be sure, there is a pattern linking the wh-complements with verbally similar questions, and this is, in fact, something found in a number of very different languages, albeit with considerable variation. But the link is made to seem stronger than it in fact is, simply by the facts that (1) English neglects the subjunctive and similar moods; and (2) picking and choosing examples given that English allows so many different ways to say the same thing, and does not require you always to say things like, "John knows who it is that went to the store" or "John knows where the place is located".
No doubt there are fields in the philosophy of language where these 'embedded questions' are of some use; but the name should not fool a philosopher into thinking that one of these fields is the study of questions.