I've seen, on several occasions, papers whose purpose it is to construct a moduli space over $\mathbb{Z}$ for a moduli problem for which a moduli space over $\mathbb{C}$ was already constructed. Let's give things names:

Let $X$ be a (coarse should be enough) moduli space over $\mathbb{Z}$ for some moduli problem. Let $Y_{\mathbb{C}}$ be the moduli space over $\mathbb{C}$ for the same moduli problem. In these papers it seems that they often say that $X\times Spec(\mathbb{C})\cong Y_{\mathbb{C}}$ (that the moduli space they constructed, when viewed over $\mathbb{C}$, is just the previously constructed moduli space over $\mathbb{C}$).

$X(\mathbb{C})$ should be in correspondence with the $\mathbb{C}$-objects of our moduli problem. $Y_{\mathbb{C}}(\mathbb{C})$ should also be in correspondence with the $\mathbb{C}$-objects of our moduli problem. However, $Y_{\mathbb{C}}(\mathbb{C})$ seems to mean sections of the structure morphism $Y_{\mathbb{C}}\rightarrow Spec(\mathbb{C})$ rather than any morphism $Spec(\mathbb{C})\rightarrow Y_{\mathbb{C}}$. This seems incongruous with the fact that it should be in correspondence with $X(\mathbb{C})$, since those can be quite weird indeed! The image of the morphism $Spec(\mathbb{C})\rightarrow X$ can be the generic point of any dimensional subscheme, whereas the image of any map in $Y_{\mathbb{C}}(\mathbb{C})$ must correspond to a maximal point of $Y_{\mathbb{C}}$.

Hopefully, you braved through the confusing notation. I feel like I'm missing something. Can any of you explain this weird phenomenon?