Nested Containers Not Aligning

I have a series of nested containers (mostly flex, with a coordinate at the base where I'm putting my components). This is starting to cause an issue with the alignment of the sizing/movement of the components that I'm adding to the coordinate container. The components will drop where my mouse is, but the box where you would normally size or drag/move the component is shoved way off into the top left corner of the view.


Ex: Red box is a label, the blue outline is the move/size box.

I am still able to use the move/size box to resize the component, but it no longer allows me to use that blue border to move the object, and I am unable to nudge it with the arrow keys, even when it is deep selected. I am able to use the x and y under the position property, but those have suddenly shrunk to very small numbers, and changing even just 0.01 can throw the component completely off the page, even though the basis of the coordinate container I'm placing it in is 500px or more.

Has anyone else encountered this issue, or know a way I can fix it?