You may have over stimulated (built too much energy) in your head (6th chakra, third eye, temple chakras, et cetera). I have known over stimulation to cause problems. In my case it was an over stimulation of my third eye, which resulted in an incredibly excessive runny nose and a build up of pressurized liquid.
It may also be an upward flow of energy (from your bottom chakras to your upper chakras) that is unable to flow out of you.
This is a part of learning.
I recommend a two part experiment.
For a week do not build energy in your head chakras. See if the pain subsides. If this does not work. Then do the following:
For a week vibrate the 'R' rune into your crown chakra because it has an affinity with movement and freedom. When you have excess energy the energy is supposed to flow up and out of your crown chakra and either into your aura of up and into the 8th chakra. While vibrating the 'R' rune visualize white light (as white in terms of light is all the colors) flowing from your crown and either into your aura or 8th Chakra. You should preferably feel a lessening of pain or of symptoms when doing this, if the problem is an excess of energy that cannot escape. Do this for a week.
If these do not work, then your problem may not have been caused by meditation or spiritual work, and you may want to see a doctor.
Hail Satan