I am a health care professional =)
Truthfully, sometimes we just do not know what causes spotting and breakthrough bleeding.
Here are some causes, and other than this we consider it a fluke occurrence.
Antibiotic use- Certain antibiotics reduce the hormonal dosage in your body, due to the interaction with the liver.(all meds go through the liver)
Missing a pill or taking it later than usual..
Saint johns wort-For the same reason as antibiotic use
Other than this, usually it is a fluke! It does not mean that your pill is not working.