Why are certain photos very dark?

Keep in mind how a camera makes exposure decisions. It sees the world in greyscale and assumes that whatever you're metering is mid (18%) grey. Then it adjusts exposure so that the "18% grey" it saw is properly exposed. If in fact that scene was brighter than mid grey, it'll be overexposed. Conversely it if was darker it'll be underexposed.

Manual mode and the histogram are your friends.

But more on point here, if it has some bright areas against a darker background (e.g., a lighted figure on a dark stage) or some dark areas against a brighter background (e.g., a silhouetted figure against snow or a bright sandy beach) it'll probably get confused by the background and miss the exposure. You might be having metering issues with bright (specular) highlights, harsh shadows, etc. I can't say for sure but unless you have your object against a backdrop that's reasonably close in value (brightness) to the object you'll have to deal with that difference.

Practically speaking, if you're going to be shooting a lot of objects (and if they're of a size that will accommodate), consider buying or building a white box. That's basically a cubicle framework with either translucent white Plexiglas or smooth white fabric walls through which very diffuse light can shine and bath your object in soft light. The object is either suspended by a monofilament line or placed on some kind of support inside the box. From what I've seen it makes for a much better "object shooting" environment than trying to light and shoot stuff on a table top.

You can Google "photographic white box" and find lots of DIY ideas, plus commercial units for sale.

For focus at this scale, you might need to focus stack.