A user of the R client we make for GBIF reports different number of occurrences for the /occurrence/search endpoint and the /occurrence/count endpoint with the same taxonkey, and limiting to georeferenced data only. See https://discuss.ropensci.org/t/rgbif-occ-count-and-occ-search-results-differ/174 for the discussion.
I imagine there's a good explanation for this, but I'm not sure what it is right now.