I am 16 years old. I started taking the pill a little over 3 months ago because I was going overseas and I wanted to skip my period. I skipped it and have been back for over 2 months, I stopped taking the pill after I came back because I wanted my period and no longer needed to use it. Once I had my period again, I noticed that there were chunks of flesh like substances coming with it. Thinking it was normal I just left it (I never used the pill before then). All went fine and a month later I received it again, this time I was trying to keep my eye out for it just to make sure, but the are still chunks of flesh like substances coming out (only when period occurs). I have never had sex but not a virgin (if you understand what I mean).
So my question is, is this normal? I have also started to bruise easier and scabing on my scalp.

I don't understand the concept of taking 'the pill' to skip a period. Birth control pills don't make you skip your period. Did you take them non-stop or something? And how many months?
And not having sex makes you a virgin, whether you insert something into your vagina or not, and oral sex is a topic for debate. So exactly how are you not a virgin? It's OK to be specific about body parts here.
Menstrual flow includes menstrual tissue, the lining that builds up on the sides of the uterus each month, to prepare for an embryo. So sometimes your flow will have chunks in it. If you have something else happening, you need to see a gynecologist. Going on and off the pill will certainly come with changes to your body for a while. As for bruising and scabs on your scalp, please tell all that to the doctor. The bruising could be related in rare cases. The scabs sound like something you picked up in your travels, perhaps head lice (just a wild guess). There's no way to diagnose online.