A common cause of headache during Qigong practice is failure to breathe smoothly. You may hold your breath without noticing it, causing Qi and blood flow to stagnate, which reduces oxygen supply to the head.
Eye ache is also common, for two main reasons. "The eyes watch the nose, and the nose watches the heart." To keep your mind inside without being distracted by what is going on around you, restrain your vision. Focus your mind in your heart and regulate Xin, your emotional mind. You do this with your mind, not your body. Don’t actually stare at your nose, a major cause of eye ache.
Your eyes may also ache when you focus the spirit (Shen) at its residence. Do this without using force. Lead the spirit back to its center firmly but gently. Mental force will cause not only eye ache but also headache.