These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Or here's a better one: If you give someone food poisoning in the 3rd and 5th editions by picking poisonous plants, you make them better by increasing rations. Huh?
It was probably meant to be a "keep them from dying of malnutrition while they flush their system" mechanism. It would have been more clear had they cut available rations by the amount that was the poisonous plants, and had several (overlapping region-specific for good measure) types of poisonous plants that would each never be picked up again once you had identified them, but hey, this was a game where a single person could depopulate the entire large-game population of the west within twenty miles of crossing the Missouri River and dysentery always resulted in huge pockmarks appeared on the affected's face. Either give them a break on the food poisoning thing, or startriffing.
Pioneers had been traveling west to Oregon for years before the 1848 start date in the game - presumably you'd be able to find a settlement in the area where your party could shelter until the weather gets better. Plus, this is Oregon west of the mountains, not Alaska or Montana - it's a mild place with a lot of rain all year round.
In the 2001 version, it will play even during events that don't hamper you, like finding an abandoned storage with helpful items left over.
Also the weird illness/injury noise. "Peggy Sue has cholera."
The hill music in II (and presumably 5) can be rather startling when you abruptly switch from cheerful trail music to dramatic, ominous, loud music.
Randal Morgan in the third edition. If you talk to him when the wagons are circled, there's a chance he'll start talking about how the "dark ain't natural." He goes on to vaguely, but with obvious terror, describe the "things" living in the dark that are trying to find him, and how he'll fight them with his fists if they ever do. It's more tragic than anything in hindsight, as it's pretty clear he has schizophrenia...when you're young, it sounds as though Eldritch Abominations are stalking the caravan.
They Changed It, Now It Sucks: A common complaint over a new add-on for the iPhone edition, if you pay real money you can buy in-game money and therefore get a higher score... or not paying more money simply means you get a lower score. Fans weren't amused.
Uncanny Valley: The cheaply animated cartoon children in the fifth edition. They're just... unsettling.
Porting Disaster: Did I ever tell you how unstable the iPad version of the game is?
When you trade or buy an ox, buffalo or cow and try to equip them, the game crashes.
When you try to post your feat to Facebook using the game, the game crashes.
The game has a memory leak problem and the entire game can sometimes slow to a crawl.
The music can just randomly stop playing.
And oh, compared to the iPhone version of the game, there has been exactly zero updates. And the iPhone version isn't Universal (read: it doesn't run at native resolution on an iPad). And to rub salt on the wound, the game's a whopping 330MB download and expands to an awesome 1.2GB upon decompression.