First of all, good for you for being prepared! While no birth control method is 100%, it is very statistically unlikely that you could be pregnant. Pre-ejaculate had either no sperm cells or only dead sperm. If he flipped the condom around prior to ejaculating, the condom itself should be fine.
There are many reasons your period can be late. Everyones body responds differently to hormonal adjustments that come from taking the pill. I am not sure how long you have been using your current brand. Also things like stress contribute to a late or missed cycle. If you go two months with no cycle, you should contact your physician.
Let me reassure you -- You are not pregnant! Be well.