I've been using the regimen for almost 2 years (almost 3) and I usually only suffer from one or two white heads on occasion. Recently I've not been following the regimen as strictly as I should and I just had a major break out. I roughly counted the number of pimple/zits on my face and currently there are 25 zits on my face. I know the regimen only works when it's followed strictly, but do any of you think leaving make-up on when playing a sport could cause an issue? If so should I just use some Neutorgena make-up wipes and gently take any make-up off. Also I've been applying concealer with my fingers, do you think that could also be a cause? Do you think I should just stop wearing make-up in general?
Ok so I know nothing about make-up because a guy, but here is my two cents. I could see how make-up could cause a breakout while playing sports or working out, here is why. Obviously we all sweat when running or getting our heart rates up. If your skin cannot produce sweat because it is blocked by something external (in your case make-up) it'll end up clogging your pores instead. Maybe you should experiment with not using make-up for a month and see how that goes. Again, I know nothing about make-up lol.
25 zits is quite a breakout while still using BP. Take a deep breath, start to follow each step exactly and hopefully you will be clear again in a month or so. I don't think the makeup would have caused the breakout, and using makeup wipes to clean off your makeup before sport may just add unnecessary irritation.
Good luck with getting clear again 
If your hands are clean and your makeup is safe for acne prone skin, applying it with your fingers should not be a problem as long as you are being gentle.
You already identified the likely problem here, and that's not following The Regimen strictly. Do your best to follow it exactly as Dan recommends each and every day. As for makeup, here are our makeup tips. http://www.acne.org/faq.html#cosmetics
and http://www.acne.org/blog/2009/04/27/makeup-if-you-must/
and
http://www.acne.org/makeup.html
Please also see Dan's workout advice. http://www.acne.org/faq.html#sweat
Hope that helps!