I’m not sure that the problem is two points being coincident with each other. Rather it sounds like the typical issue of having two features with the same feature ID. When both are added to a topology then it becomes ambiguous as to which feature should be used (so neither are used). It usually happens when a feature is copied (rather than cloned) such as when a GPML is copy’n’pasted (and so the feature IDs are also copy’n’pasted).
This post has more information.
I’m not exactly sure how you copied - you do mention a copy but it also sounds like there’s only one feature added to the topology. In any case, feel free to send me some example data that reproduces the problem.