The GraphML standard is mostly about defining the structure or 'topology' of a graph, roughly speaking the set of nodes and their connections/edges. Additionally, there is a very generic attributes extensions which describes how to add data to nodes, edges and the graph as such.
However, the standard does not define how geometry data (e.g. node sizes and node locations) or visual properties like colors and/or labels have to be represented in GraphML.
Thus, each application that wants to store geometry or visual properties in GraphML has to come up with its own (sub-) format to store these important properties.
So, if you open a GraphML file that was not created in yEd, yEd is able to read only the structure of the graph from said file but nothing else. In such a case, yEd will use default values for the style, location, and size of all nodes. This means all nodes will look the same, have the same size, and will be located at the same point.
To see how many nodes and edges there are in your graph, run one of yEd's layout algorithms. "Layout" -> "Hierarchical" is usually a good choice, if you do not need to highlight specific structural properties but only want to resolve node overlaps.
