I think this is a fine education question, particularly because teachers and students should be communicating clearly and correctly to each other.
I suspect "subtract 4 from 3 times X" is ambiguous enough for most readers that we might choose to avoid the operation words (subtract, times, etc.) and use noun phrases. If the arithmetic expression you're after is $3X - 4$, then a clearer option might be "The difference of $3X$ and $4$". Here, you're more clearly separating the the objects (the terms) being subtracted by using the word "and". Similarly, if you want to describe $3(X-4)$, then you could say "the product of $3$ and the difference of $X$ and $4$" -- Kind of awful to have to say, but not ambiguous. The factors (parts of the product) are each clear objects themselves: $3$ and $X-4$
Answering this from a teacher's perspective, I would avoid saying anything like this out loud (if at all possible) without also showing the relevant mathematical expression, unless it was something extremely simple (such as "5 plus 2"). After teaching a section on this topic (translating Math to-and-from English), my students always come away thankful that we can actually use symbols instead of having to be so wordy. However, whenever we happen to read a mathematical expression out in words, I am always taking the time to (try to) make the phrase unambiguous, or I'm pointing to the particular symbols.