Were they pills? It could be a reaction to the filler materials. My mother-in-law couldn't take generic meds supposedly because they used lower quality filler materials, and she would have an adverse reaction. Personally, I think it was psychosomatic, but I never tried to prove that.
Since homeopathic medications are diluted to the point where there is a near zero probability of their being a single molecule of the medication remaining in the pill, there would be nothing of the active ingredient for you to react to.