Dark sides of the main characters... I should point out beforehand that I don't see anyone of the dark sides of the characters I am going to list as strong enough for them to actually deliberately abandon their good nature and turn all Darth Vader or would intentionally do anything that would inflict actual harm to any of the others (while they might perhaps do so unintentionally or through the manipulation of others).
In case of Littlefoot it is that he has a very hard time to see things through the eyes of others when their view differs from his. Littlefoot is a very well meaning and idealistic character, but his idealism comes at the expense of his ability for compromise or diplomacy whenever he sees his personal sense of justice violated. More than once we have seen Littlefoot standing up for points which usually turn out to be just, but ignoring quite legitimate points of others (sometimes the point of risking their lives for something or someone about that / whom they don't share Littlefoot's enthusiasm). Littlefoot rarely makes elaborate attempts to convince anyone, but "leads by example" (worded nicely) or "forces the others to follow by dashing of into potential danger on his own" (worded a bit more down to earth).
In case of Cera the darker sides are quite obvious. A degree of quarrelsomeness, irascibility, boastfulness and pride that makes it difficult for her to admit failure... these can (and have been) sources of trouble.
Ducky is of course one of the most easygoing of the gang. This too however can be problematic. She would rarely stand up to the others in case she is really convinced that whatever they are about to do is wrong. Her extreme desire for harmony (something I can very well relate to) can make her somewhat naive and bears the risk of her being taken advantage of not just at her own expense, but possibly at the expense of others too. We got a rare glimpse of a darker side of her in the TV series episode about the sky color stones; where her perception of luck and harmony may be infringed by others such sneaky side of hers may come up.
Several of Petrie's "dark sides" are similar too Ducky's. He too is not often the one to speak up against the others but for the sake of what may be seen as a major problem he is often struggling with, his fearfulness that may sometimes lack basis more solid than superstition. For that reason he too can be (and has been by Pterano) manipulated. Petrie is aware of both the naitivity ("me believe everything") and his fears and would probably like to overcome both and earn some more respect and recognition from some of the others (maybe Cera in particular). Such harbored but hidden sentiments might manifest into his acting against better judgement at some point.
Spike is possibly the most down to earth of the entire gang. I don't see him getting manipulated into any complex schemes of any kind. He is so easygoing and forgiving that he doesn't hold the kind of grudges about something that might be at work in case of the others. There is only the gluttony of his which has more than once gotten the better over his common sense even though he never intended any of the harmful results.
I do not see Chomper turning against his friends. It is a popular idea and of course laws of nature dictate that when he grows up he won't be able to live on a diet of butterflies anymore. I do not however see natural instincts taking so much control over him that he was to be incapable of making any difference between which prey to go after. Maybe he could make do as a scavenger (as many lions do). Chomper is a rather sensitive character and this might in fact work very much against him come the day that he is to become an actual predator. He doesn't seem to have the kind of temper that would make him loose control as easily as in case of Cera (Chomper would likely react with sadness rather than fury in many cases). I see the potential of him getting seriously hurt by continued (or increasing) reservations and distrust against him, but I also see him as capable of appreciating the extraordinary nature of the degree of trust he receives from the residents of the Great Valley. Odd as it may be, I see him as a character whose "dark sides" beyond the bear necessities of nature may be much more difficult to bring forth than in case of some of the others.
We know relatively little about her. In spite of her cheerful and inquisitive nature she bears a streak of melancholy which none of the other characters shows (something that might befit Littlefoot with regard to his mother). Said melancholy however is something that Ruby is mostly dealing with herself. Could she get actually depressed and react over the top if facing a lack of sensitivity at that time? Perhaps so, though she too comes across as someone with a lot of self control to keep in whatever dark side there may be. But keeping in may not always be the best way of comming to terms with that side.
I admit, Cera and Pterano have a lot in common. I mean, she kept going and the Gang of Five could have died because she blundered them into the Mountains that Burn even though Littlefoot told her to go otherwise. Had they listened to him, they wouldn't have gone in there at all. She keeps going even after Petrie falls, yes, it was by accident. She doesn't bother to check for the others either and they all would have died had it not been for Littlefoot (whom she felt was inferior.) If the others died for her pride, and she were older, one wonders if she would have gotten the same punishment as Pterano.
And, on that regards, she doesn't ever seem to see that in Stone of Cold Fire and think "Well, I was a knucklehead in the Mysterious Beyond and almost got you guys killed. I can feel for the guy."
While I can understand why Cera would be ticked that Littlefoot is nicer to Ali than her and that Ali has been snubbing the the non-Longnecks, I can't see why she at first refused to go with Ali to help Littlefoot.
As for Chomper, I can see a scenario that could really put him in a bind. He's kind-hearted and that could lead to trouble. What if he gets a Sharptooth girlfriend, one he got to be nice to leaf eaters, but someone in the Great Valley sees her, doesn't know too much about her, and overpowers her and tries to kill her? He might end up having to take a leaf eater life to save her. That could lead to a problem, once he's actually killed a leaf eater, he might feel that it's too late now or feel conflicted and his dark side could come out after being held in for years. Also, he does appear to be stalking the Gang of Five in the fifth film as he should have tried to get their attention when they ran, other than doing what he did. Even his look shows he was going to kill them, or almost implies it, before he recognized them. (Nobody has brought up why he chased them. True, they were cowering with their eyes closed (a huge flaw on the Gang of Five's part as they did the same thing in II also and that could suggest that it never occurs to them to make a brave last stand or whatnot if they are cornered. ) but they had to wonder, especially doubting Cera, what was going on.)
Ducky, her behavior in Sky Color Stones was truly shocking. I mean, she ignored Spike and was hoarding those stones like Gollum. She even had trouble letting one go, even at the risk of her life. Also, let's not forget that she told Spike to go away in film VIII.
As for Littlefoot, another thing he did was that he got Cera to try and break that big stone, saying he'd dreamt it, which I think we can safely say was a lie. Though good for her to get humbled, I think he could have gotten her hurt.