I am hesitant because I am not sure this is the right forum for your question or that we can offer a properly sourced answer but until one of those two questions are answered I will suggest the following:
Insofar as it was typical under most circumstances to refer to someone as the son of their father, the deviation from this norm would likely raise question and/or not done for naught. Consequently it seems reasonable that someone reflected on how this would be received and hypothesized that it would imply a question of paternity. Subsequently this hypothesis was passed along without any indication of its speculative nature.
While this hypothesis isn't entirely unreasonable it is worth emphasizing that it is likely speculative (after all, your asking the question implies your source didn't cite their evidence). Insofar as Joseph is said to have originally intended to divorce Mary quietly (and ultimately married her) it is difficult imagine that he or Mary chose to publicize any questions about paternity. The traditional prohibition against remaining married (and "betrothed" was a form of marriage that required divorce) to an adulteress (see Mishneh Torah: Gerushin 11:14) would have likely led to Joseph's continued marriage to Mary as taking responsibility for the pregnancy.
Furthermore, we have to remember that this type of nomenclature is descriptive. In colloquial use it would make more sense to describe someone as the mother's son when those listening are acquainted with the mother and not the father (in the same way we would identify someone by their relations today).
Finally, insofar as the author of the selection you have provided did not include the background story about the Nazarene's conception it is hard to imagine he was obliquely referring to it here.