The use of along with in this sentence could be read as if you bound "Python, along with its related packages numpy and scipy" together into a group of undifferentiated members, as one might write "Flour, along with sugar and baking powder, are used to make a cake".
While you may have intended the sentence to emphasize Python's role making the statistical analysis with numpy and scipy taking secondary roles, your colleague may have read the statement as emphasizing the use of all three members of the group, along the lines that Python, numpy, and scipy are used to make the statistical analysis, thus missing the hierarchical relationship among the three that you may have been trying to imply.
Consider a sentence that clarifies that hierarchical relationship, such as Python, enhanced with functions imported from the numpy and scipy modules, is used to make the statistical analysis