Well, I do not think that it's a glaring error. My thoughts are that he is in the shadows for the purpose of suspense.
When Littlefoot started pulling on that cycad (or fern or whatever)
something started to make a noise. We as the audience know it can't be the plant, so we start wondering what could be making that noise, and then this strange looking sillouetted creature falls out! After that bit of surprise, we are introduced to our new friend Petrie, who is now in the sunlight where we can see him clearly.
So mainly, I think that the filmmakers wanted to introduce the "comic relief" character in a slightly different way that was suspenseful and humorous.
This is just my two cents though.
