Vit. D deficiency has to addressed properly by taking regular medications but to my knowledge vit. d deficiency can never lead to pain around yours at this age , yes you can get generalized weakness but not pain. the reason of pain around your knee cap could be something else, may be you are getting delayed onset muscle soreness if you are focusing only on your knee exercises, may be your muscles around your knee are stiff which are not able to cope up the stress during exercises, may be you have hurt your knee but for this you need to be thoroughly assessed.
Next Steps
use hot packs thrice a day around your knee joint to reduce pain and relive the stiff muscles. you can apply any local ointment or spray around your knee cap before and after the exerises. and if pain allows you can start with the exercises under physiotherapists guidance
Health Tips
Do not rush on with stressful exercise, gradually modify and add on the exercises