- Are you using pg_repack? I'm fairly sure its logic has some holes - last time I checked its bug tracker listed potential for data corruption that could cause issues like this.
- Have you done OS upgrades? Did affected indexes have any columns affected by collations?
- Have you done analysis on the heap page? E.g. is there any valid data on the page? What is the page's LSN compared to the LSN on index pages pointing to non-existing tuples on the page?