This problem appears to have started with Revision 9185. Incidentally, the problem with Native Culture (Neanderthal) being given to "regular" civs (in addition to their normal native culture i.e. (Oceanic) or (European)) also appears with this revision. Presumably the problems are related and the promotions are available because of the same conditions that are incorrectly giving the neanderthal culture to all civs.
(I went through a bunch of older revisions until I found one where they stopped happening, then shrank the gap until settling on 9184, where it didn't appear, and 9185, where it did. Someone else should try confirming as well, in case I made a mistake somewhere.)
Based on the files, if I had to guess, they're getting TECH_DUMMY_NEANDERTHAL, but I don't really know how since I'm not familiar with the intricacies of Civ4's XML, nor am I able to find any reference to that tech in a way that doesn't directly relate to the neanderthal civ.
.
Incidentally, I also noticed the issue about how great people (at least great generals) increased on cost, as was mentioned in a previous post. In my testing games, some of the early revisions (dated around Feb) cost only 25 'experience' for a great general (normal speed, dual map) whereas they currently cost 75 experience. Unfortunately, I didn't think to try tracking this until much later when I was closing on the promotions issue, at which point they were all the same increased cost. I'll try zeroing on this one as well.