The phrase having a "Good face day" is reminiscent of having a "good hair day". A "good face day" occurs when someone's face (usually pertaining to a female) is looking especially nice. This can be used as a casual compliment. Telling someone they are having a nice face day does not mean that they do not usually look good, you are just saying they look extra pretty.
Although less common, the phrase can also be used in the negative; as in a "bad face day". However "bad face day" is only used by someone talking about him or herself.
A: "You are having a good face day"
B: "Thanks, I wasn't running late this morning so I had time to put on my makeup."
A:"Ugh, I am having such a bad face day!"
B:"What do you mean?"
A:"Do you not see the huge pimple on my chin and the bags under my eyes?!"