I have been there too. Double IT A'level and poor maths and science.
The verdict
Civil = No problems with self sponsorship, however schemes like Flybe MAPS and other mentored schemes prefer you to have 2 of Maths, Physics, Science or English to really be considered. CTC Require two A'Levels from most subjects, inc ICT/IT, but they are going to prefer Science, Maths and English, same as they prefer a degree but dont say it.
Mil = Again, to be a pilot, from what i can make out, if you dont have maths, science or english you are at a disadvantage when applying to be an Officer, Flight Crew or other technical trades.
So i would say, no you havn't messed up, your young enough to go back and take the subjects you need and move on. At 22 i have had to, so at 17 i am sure there are no issues, you could get your A' and a degree by the time you get to my age, and all i have is IT subjects and Business. I am taking Mechanical Engineering BEng and doing three alevels.
Your qualifications however in most cases just get you a foot in the door. Remember all the RAF Battery Tets, Personality Tests and whatever else they do. Your personality will also play a part in getting that job.