The problem is that the Spanish sentence is using the preterite tense here, so Duo expects you to answer in simple past.
The sentence construction sounds a bit wrong to European ears. Normally a word like "already"/"ya" is a pretty strong indicator that the sentence has relevancy to the present, so the present perfect, "have eaten"/"has comido" would be more appropriate. But apparently American Spanish allows such a construction with the preterite.
This is one example of why I'm really concerned about recommending DL to anyone whose English is not their primary language -it can confuse or wreck their English usage and English grammar.
I can understand that a literal rendering can help us 'think Spanish' and 'think Spanish grammar'. So here I offer "Did you eat, already?" or, better,
"Have you already eaten? (Literal: Did you already eat?"
like MarieRose131947 I was marked down for inputting ' Have you already eaten ' which is perfectly correct english.
According to google "¿Usted ya comió?" translates to Have you already eaten?
and ¿Usted ya ha comido? also translates to Have you already eaten?
while ¿Ya comio? translates to Have you already eaten? or "Did you already eat?" Did he already eat? Has he already eaten?
British english speakers would generally use "Have/Has" and not "Did" except perhaps in the negative "You did not eat already?"