Thanks for the query.
According to your history, the possibility of pregnancy
As you are taking the pills regularly at same time every day.
By using regularly, pills can offer up to 99% protection.
Some amount of menstrual irregularity is common while being on pills.
The spotting could be due to hormonal
And the brown color could be due to collected blood in the endometrium as you told.
So, no need to worry.
Possibly the spotting will turn into normal flow soon.
And you can start your next pack as usual.
If you missed any pill completely by chance, then go for pregnancy test once.