How is Lizzie somewhat meek, naive, or too innocent? If not any of these, are there any negatives of Lizzie's character?

In Charles Dickens's Our Mutual Friend, Lizzie Hexam is a character completely marked by her tendency to sacrifice herself for others. Whether this is a mark of a strong and caring character or a sign of meekness to a fault is entirely decided by the subjective observation of the reader. People, particularly men, who lived in the time that the book was written, and perhaps even Dickens himself, likely held Lizzie in the esteem of a perfect woman. However, more modern readers, particularly those who would read through the feminist lens, might raise their eyebrows at some of Lizzie's choices.
The first and most glaring sign that Lizzie's devotion is perhaps more of a sign of meekness than of strength is her devotion to a man like Gaffer Hexam. Gaffer is an uneducated man who makes his living robbing corpses out of the Thames river. Even though Gaffer treats Lizzie absolutely horribly, she remains devoted to him. She even goes as far as to refuse to learn to read and write, despite having a strong interest in it, simply because she worries about the divide that it will create between her and her father. This definitely seems like the sort of sacrifice that would be born out of meek fear, rather than out of true loving devotion. Lizzie believes that she can make her father change his ways. In fact, she often comforts herself by thinking that her father would be much worse without her around to help him. She admits that she doesn't know how she'll do it or what cue she is waiting for, but she keeps faith that a moment will come in which she can "turn him to wish to do better things." This certainly reflects a degree of naivete, as everyone believes that Gaffer is irredeemable and responsible for the murder. Lizzie maintains that he has been framed, amidst a sea of doubt. Ironically, she is right. It is worth noting, however, that Lizzie does defy her father somewhat in her decision to send her brother away to be raised out of a life of low-class poverty. This decision to spend her carefully saved money on Charlie is repaid with selfishness and abandonment. Still keeping her head up when she is caught between her brother's selfishness and her father's proud ignorance, it is in these moments that we see a Lizzie who is unbreakable and simply wants what is best for her family.This brings us to the answer to your question. In the work itself, while we in the modern world could certainly make several points for Lizzie's meekness and naivete, her intuition is seldom wrong. Her intuition about her father's innocence was correct, she is never cosmically punished for her devoted nature, and it is quite clear that Dickens intended her character to come across as pure and moralistic rather than meek and naive.