My guess is that these large spots are from coupler dispersion globules whose size are well outside the standard deviation of normal coupler dispersions.
Yup, and AFAIK Harman has also acknowledged this issue.
I suspect that the root cause is to be found in the emulsification process employed by Harman. The chemical backstory is that although we talk about 'emulsions' all the time, from a chemical viewpoint, a silver-based gelatin 'emulsion' is really mostly a solution of gelatin with some other stuff mixed into it. The caveat is that in color films (and paper) there actually
are emulsions in a literal/chemical sense: the dye couplers are oily molecules and they need to be somehow worked into the gelatin-based 'emulsion' (which, as said, is in its basis really a solution and not an emulsion - yet) without the oily couplers separating out and drifting on top of the watery part.
So a step of emulsification takes place, in which the dye couplers form minute globules that are suspended in a gelatin-based solution - making it an actual emulsion (i.e. an oily substance dispersed in a watery solution). Ideally, this coupler emulsification yields globules of a small, consistent and predictable size. I think we're talking in the order of magnitude of single-digit microns or something thereabouts, but don't quote me on this...
Apparently at Harman, the current emulsification process isn't quite as well in control as it is at e.g. Eastman Kodak or Fuji and they end up with a proportion of too-large globules. These show up in the negatives and this in scans, prints etc. To the best of my knowledge, this presently mostly happens with the magenta coupler. I've indeed seen it in Phoenix as well, but haven't looked for it, and as a result, I've only seen one or two really big (relatively speaking) of these defects. It doesn't surprise me that they actually occur more frequently if you systematically look for them.
This is one of the many things Harman will have to iron out on their journey towards a mature/regular C41 color film.