Not all spotting disrupts the clean days. For example, spots smaller in area than a gris (roughly, the size of the American dime or Israeli shekel) do not invalidate the clean days. The status of spots larger than a gris would depend on their shade. Yellows and light browns with no hint of red do not disrupt the clean days. Pinks and browns should be evaluated by a rabbi. Red will generally disrupt the clean days.
Your wife may be able to get through the clean days by changing her underwear more frequently, to reduce the likelihood of larger spots accumulating, and by having any stains of questionable color evaluated. Additionally, in cases such as these, there is room to reduce the number of bedikot to one a day and to wear a white pantiliner, which may provide grounds for further leniency.
If these solutions do not suffice, there would be a possibility of further reducing the number of bedikot, and colored underwear could be considered. In this case, please get back to us. Alternatively, you could contact the rabbi who permitted colored underwear in the past to ask about the current situation.
It often takes two to three months to adjust to a new hormonal method of birth control. If the staining persists, your wife could consult with her physician about ways to reduce the staining.