I just had another difference between Stardew and real life occur to me: squirrels and rabbits. Also crows.
Those cute little squirrels and rabbits that periodically dash up or away from trees in Stardew are, in real life, an utter menace to gardens. They will eat your plants, dig them up, randomly bury other seeds in your garden bed (I have so many oak seedlings popping up in mine right now!) . . . they are terrible, evil little garden chaos monsters. Crows, on the other hand? The worst problem I've had with crows is that they will try to hide food in my garden beds by placing it on top of the dirt and covering it with leaves or dried grass. Very, very occasionally one of my crow neighbors gets into a snit about something and yanks at one of my plants while yelling at the top of his/her little crow lungs. They don't really bother the plants or seeds otherwise, though. Not like squirrels and rabbits. My husband has a vendetta against both; the only reason they're safe in our yard is that we live in the city and we are not allowed to take them out (and eat them; both are pretty tasty).
This does depend on region mind you, here in the Columbia Gorge I have had few problems with squirrels and that is mostly because of the strategic placement of the farms I've worked on, usually near large cliffs or water, where the squirrels are much more content interacting with their natural habitat then even coming close to the human farm, though having worked in many different farms I completely know what you mean, squirrels can be a hell of an annoyance, crows I've only had major problems when on larger farms, I used to have scarecrows dressed as British redcoats in my old farm, however, crows are smart little bastards and this only worked for a little bit.
Also, coyotes, wolves, and coyotes, and maybe raccoons, which are less a danger to crops and more a danger to livestock.
Here in the Gorge, (And most of the Northwest) it is prime living for animals like wolves and coyotes, I still remember having a mini heart attack whenever I went to bed and suddenly question whether I closed the doors or not, and I would run outside to see that I indeed did close the doors. In Stardew Valley I still close the chicken door and barn doors just out of habit even though in the game it doesn't matter...to my knowledge anyhow.
My current garden is closer to town so I don't have to worry about coyotes and the like, however, raccoons are still a problem.
I've returned to this after a while and I'm glad to see a few other farming folks to give their input, it is such a joy. I got reminded of this place after seeing an article written about this thread, which while I was embarrassed upon seeing it, sure it also motivated me to come back here.