From looking at the code, it seems that muted topics are supposed to be excluded from the summary email. Note that it is muted topics that are excluded, not topics that are in muted categories. Where this could be significant is if a user who has muted a category has interacted with one of that category’s topics in a way that would set their notification level for the topic to anything other than muted. This would happen if the user had replied to the topic prior to muting its category, or if the user had spent time reading the topic, or replied to it after having muted the category.
Does the above explain what you are seeing for this user?