Most players will see a warning icon and take that as an instruction that they need to do whatever is necessary to remove it to avoid bad things happening. Some players will ignore it until something actually bad happens. Unfortunately the way warning icons in this game work is suited to the latter minority far more than the former majority. Through a bit of reckless disregard I’ve learned to see many of the warnings as signs that everything is working well.
Food lost to decay. If your food supply rate is larger than your food consumption rate, then no matter how long you preserve it you will see the difference rot. This is a good thing, it means your supply is adequate. If you are losing no food to rot, then your food supply is insufficient and you’re in for rough times. I aim for about 5-10% rot as a good buffer.
Dry wells. Villagers will collect water from the closest available source, which means the most central wells will always run dry. They will be filling as fast as their little stones can manage, and operating quite well though. So long as there are more wells slightly further away to pick up the demand when the first is low then everything will run just fine.
Crops eaten. Baiting wildlife with farms to then hunt them is fairly effective. That little crops eaten warning means things are going to plan. Ditto for herds grazing.
Storage full. Again, a sign that things are going to plan. So long as your production limit matches your storage capacity this is a sign of things working well.
No swords on guards. Yeah, my towers are there for shooting, not stabbing.
Villager attacked by wildlife. I have a boar farm, so I actually get worried if I don’t see this warning a couple of times a year.
Rats infestation. In warehouses without food rats have no effect, I just ignore them. In cellars and stuff they always pop up to trigger your rat catcher to go thump them. The warning is once again a sign that things are ticking along normally.