The ideal from the start was that the taxonomy would be a "partition" of mathematics -- that every problem would belong in exactly one place. This is difficult because lines between areas can be blurry, but it was confounded by confusing a classification by topic with a classification by relevant course. Often, more than one mathematics course will cover the same topic.
Our plan to deal with this has 2 parts. First, we stick to the original ideal of trying to partition problems by mathematical topic. Then, we build into the OPL/library browser the ability to cross-list problems. Cross-listing would be at the level of sections.
For example, in the first pass, we expect to have "algebra" (which includes college algebra) and "trigonometry" as subjects, but do not forsee having "precalculus" as a subject. We then use the cross-listing feature to take sections from algebra and trig to make a precalculus subject. To the user (the instructor), this will be transparent -- it will be as if those problems were tagged to appear in two different places. The change is in implementation where we are picking something we think will be easier to maintain.