I think I may have figured it out. Your listings are from sandicor. Anyone using a realtor not based in San diego would probably list in their mls, thus not showing up in your search. Somehow redfin pulls from all the regionals. I think downtown condos or other areas with investors from areas out of town, would get missed by your site. Same with repo clearing houses. The repo I bought was listed out of L.A. by a realtor working for a particular bank, who had all their listings in so cal. That happens frequently.
As an experiment i compared downtown SD using your website and redfin. RF had 452 actives (excluding pendings, which was another 119) in 92101, you had 300. I excluded shorts on redfin and still got 332. So excluding pendings and shorts, your missing listings, as a consumer I’d like to see them all and I’ll decide. Based on my little experiemnt, 1/3 of the downtown listings are not using sandicor, or at least they are not getting onto your website.