In world war 1 were the hospitals clean?

Yes. There was tremendous difference between the hospitals of the American Civil War and the Crimean War and those of the Great War. The germ theory of the cause of disease had been discovered, and the importance of cleanliness was understood.

There were no miracle drugs to fight infections though. Penicillin would only be discovered on the eve of the next war. Wounded men endured unspeakable pain when the "agony wagon" was wheeled through the wards, so the doctors could drip Dakin-Carroll solution into their wounds and trim away necrotized flesh. The only effective painkiller was highly addictive morphine. Most men were able to "get the monkey off their back" and quit the morphine, going through withdrawal as soon as they could stand it. Many never could shake the addiction and returning wounded were the first great wave of those addicted to narcotics in America. The only anesthesia for surgery was ether.