I've been on mini pill a mth now, had my period for 3 days, missed pills but next day I got cramps & clear vaginal discharge, negative hpt, the cause?

Missed pills. The uterine lining is dependent on the hormonal influences on it. If on birth control, the amounts and types of hormones have varying effects on the lining and its shedding. Any time a pill is missed the sudden change in hormone levels can result in intermenstrual bleeding or breakthrough bleeding or increases in cervical mucus. It is important not to miss or skip any pills.