It might be the time zone your in. most of your ponies are to be born at 00:00:00 check the clock on the top. The time zones PI is in might be different from yours.
Note the time and date in the upper right corner of your screen. The time on PI differs from that of your time zone. The babies will always be born when the time that your nursery says the babies will be born matches that time. PI did not have an error. In nearly three years on PI, I have never had ponies born even one hour early. They always come the hour exactly 5 days after you mated your pairs.