Thanks for the query.
Some amount of hormonal
fluctuation is common while giving the breast feeding.
That may be responsible for your irregular cycles.
Brown colored blood usually indicates collected blood.
As you are taking, progesterone
only pills, if you forget to take one pill, that should be taken within 3 hours.
If you miss one pill completely in one day, the protection can not be expected.
And you have to use additional contraceptive
method for one week.
For more details : http://srsree.blogspot.in/2013/12/guidelines-for-usage-of-progesterone.html