Here is a hypothetical conversation where emphasis on did might make sense:

Speaker A: "You look sweaty. Were you working out at the gym?"

Speaker B: "No, I didn't come from the gym."

Speaker A: "Well, where did you come from?"

Speaker A wants to elicit an affirmative statement by that emphasis. The emphasis also serves as an indication that Speaker A is a bit upset by Speaker B's uninformative negated response.

Here is a hypothetical conversation where emphasis on did might make sense:

Speaker A: "You look sweaty. Were you working out at the gym?"

Speaker B: "No, I didn't come from the gym."

Speaker A: "Well, where did you come from?"

Speaker A wants to elicit an affirmative statement by that emphasis. The emphasis also expresses annoyance at Speaker B's uninformative negated response.