Collectively, they actually knew a bit regarding the visible contaminants; but compared to a modern person it was rudimentary and lacking for obvious reasons - such as no scientific method, epidemiology, germ theory, or any idea in general about microbes and pathogens. What they could see or smell, they knew was bad. The area of misinformation, even if correct, was the things they could NOT see. In short they missed that crucial connection which lead them to believe that the air or water directly around disease was the problem, not the microbes permeating in it. A lot of what they attributed to causing illness was miasma/malaria theory - pollution/bad air. Now this might sound like an overall positive outlook towards medieval people and disease, but don't be mislead. There was little consistency in education and knowledge and combined with necessity and scarcity, people risked what they could to survive.

In contrast, there were those that had cultural and spiritual customs that many also outright believed in illness being the work of supernatural entities. It wasn't uncommon for folks to believe in divine moral judgement to strike someone ill or deliver an epidemic.

This also doesn't mean that these ideas were mutually exclusive. Someone could both know practical knowledge but also superstition. As far as prevention and understanding, there were not many advances over previous Roman understandings (of which the medieval era was actually contemporary with the Eastern Roman Empire).

So the cohesion for high level sanitation of a military encampment, which is temporary by nature, was difficult. They knew disease could destroy their military efforts. No sewers, at best latrines, often times dumping waste into their own water supply (if it wasn't a well). They did know they were supposed to fetch water upriver from where they dumped waste. The problem was enforcing this was inconsistent and army camp conditions could lead to contaminated water. People absolutely need water so they are going to drink it anyway, and while some knew boiling could 'cleanse' water, if they didn't see or smell anything wrong with it then they had no reason to.

Regarding aforementioned cleansing, they the idea of hospitals and separate wards was still developing, but they did gather the ill in one place and often the clergy would attempt to purify the air to chase away malaria/miasma with incense and oils. They would even use scented cloth over their faces to prevent disease - but the efficiency is questionable. The reason they did so was they thought the scents were helping, not the physical barrier.

They obviously knew not to eat something rotten and that dead or rotten things could spread illness, but again they didn't know WHY. Just that dead was bad and spread death.

A simple example was a retreating army dropping a dead goat into a well. This was known as poisoning the well and medieval people knew this tainted the water. They didn't know it was contaminating microbes spreading in the water causing the disease. If the water was bad, they could figure it out, the problem was by the time they realized cholera or dysentery was spreading a lot of people are likely to have drank that water. A counter logic to this was that sometimes they did not suspect the water because it had been fine for a long time and nobody got sick. Without any sensory cues, they couldn't comprehend the microbial changes in the water.

Further trouble was that soldiers weren't always in the health on campaign. Malnutrition and hunger was common, which makes humans more susceptible to disease due to weakened immune system. The common cold could kill. Pair this with the elements (heat/rain/cold) and cramped, unsanitary living quarters and disease can catch on and spread easily.

Believe it or not a lot of the preventative methods, problems and remedies were the same as late as the American Civil War.

The Crusades: A History by Jonathan Riley-Smith (contains a few passages regarding disease and famine)

https://oll.libertyfund.org/titles/hippocrates-the-writings-of-hippocrates-and-galen (Like most medieval physicians, I'll be referring to Galen and Hippocrates!)

The Black Death: The History and Legacy of the Middle Ages’ Deadliest Plague