Can taking microgynon different times of a night effect the protection? and a possibility to be pregnant?

Usually not.: Birth control pills are more effective when taken the same time of day consistently. However, that doesn't mean the same exact time each day. It is best not to vary by more than a few hours. If you do miss taking a pill, it is best to use a backup method of contraception, like condoms, for several days until you have gotten back on track taking the pill.