It's very reliable--but you have to follow the "rules" of NFP to get the effectiveness results near 99%
WIth Billings- one of the rules is sex every other day leading to the appearance of fertile mucous-as well as evenings only on those days to ensure it is an innfertile day, precisely for the reason you mentioned
Interestingly when the fertile mucous is about to appear, it actually has spermicidal qualities- which I find fascinating (because I am a nerd like that!). So if a woman is having an infertile day, has sex that night- and then fertile mucous begins the next day (which will be masked by seminal fluid)- she is still nearly 99% unlikely to get pregnant because of this quality of the mucous.