If the rules cannot be followed on a chip, might i suggest going to design rules up the top and setting them up to what your manufacturer can reproduce, if a chip is too small to meet these rules, then they will not meet the manufacturers requirements either,
From your list with the multiple REF** entries, i would say you have added parts manually rather than at the schematic level, and as such lacks a netlist entry, on the left side of your image it would appear you have manually added stitching via's,
To better do this, there is an option on the left edge of the program to turn off delete old tracks, this way you can via stitch without issue, under general you can also turn off magnetic pads and traces if you want to place them in arbitrary positions on the traces,
some of the other errors i would need to see the log to decode for you,