Earlier today, I used the proofreading feature on a message, and it decided that the end of the quoted sentence should end with a comma instead of a period.

This feels like could be caused because it ignored the quotation marks? I'm not too sure.
The quote was used in the middle of the sentence, and if the quotation marks weren't there, the comma would have made sense.
I expected the proofreader to let this pass, as the quote was a full sentence which ended with a period.