
Welcome to InkscapeForum!
Aaah, I can see that you are well on your way with Inkscape!
What happens is that by default (so when you first install Inkscape) all the shapes and tools have their own styles. But in Inkscape Preferences, they are set for "last used style". What that means is that the first time you draw, for example a rectangle, if I recall, it was pink and partially transparent. But chances are you don't really need it pink and partially transparent, so you change it to whatever you need -- let's say green and opaque. Because of Inkscape Prefs being set to last used style, the next time you use it, it will be drawn green and opaque. So whatever tool you used to draw that, I would guess that the last time you used it, it was opaque. So that would be my guess how it happened.
With Inkscape though, one often might have many, many objects on top of one another. It doesn't really work to use partial transparency to see which one is on top, if there are more than 2 objects stacked up like that. The Alt key is really helpful here. With Alt + click, you can select objects that might be one or more levels down below the one on top. That works with the Node tool and Selection tool. If it's gonna be a really complex image, you might even use Layers to keep things organized in the z-order. Then you can actually hide layers to see what's below, or to make it easier to select things.
In Inkscape Prefs, you can set each tool to have its own style, if that would work better for you. I actually prefer it that way. Because almost never do I want whatever I draw to have the exact same style as the last thing I drew. I have all my tools set to draw a black, opaque stroke, with no fill. Except for the Paint Bucket tool, which has an opaque fill and no stroke (because I almost never need a stroke on a path made with Paint Bucket tool).