Does bleeding from the body, such as from wounds, invalidate ablution?
Bleeding doesn't invalidate person's ablution. And Allah Knows Best.
What should a praying person who doubts having offered one, or two prostrations in the third Rakah (unit of prayer) do?
Whoever has doubts about their prayer should consider what is less i.e. the above person should offer another Sajda (prostration) and complete his/her prayer, then offer Sujood As-Sahw (prostration of forgetfulness). And Allah Knows Best.
Is it permissible to offer Istikhara prayer (seeking guidance) after Witr Prayer (A confirmed Sunnah which is offered after Isha prayer and before Fajir prayer with a minimum of 3 Rak`as and a maximum of 11)?
It is permissible to offer Istikhara before and after Witr prayer as it is permissible at any time except that in which prayer is disliked. And Allah Knows Best.
A woman used contraceptive pills, and her menses exceeded (15) days, is it permissible for her to fast?
The maximum of menstrual blood is (15) days, but if it exceeded that due to a medication, or the like, then it is Istihadah (bleeding outside the monthly period), and in this case she should perform Ghusl (ritual bath), pray, and fast. Moreover, she is obliged to make up for the missed fasting days which exceeded her regular menses. And Allah Knows Best.