Seems like there is some disconnect with the defined spatial reference and how the spatial points are being created.
There are different ways to create input point layers from a set of coordinates if you have them without doing it manually.
Check out the Make XY Event Layer tool if you have a list of X,Y coordinates. Can also take advantage or convert Excel To Table (Conversion) tool. You can then use Project or CopyFeatures (with environment setting) to set the appropriate coordinate system for you final output.
If you are continuing to have issues I suggest contacting Esri technical support to help you with your data and your process.