And, to finally answer the original question: For all of the reasons given by various contributors above, it was considered to be an unwritten rule at the FCC in those early days to have the maximum allowable allocations in the biggest cities. In most cases, that was 2-4-5-7-9-11-13 (or a variation on same), because adjacent channels could not be used in the same geographic area; the extra gap between channels 4 and 5 allowed for seven allocations in the larger metros.
But in actual practice, only New York and Los Angeles had that exact "perfect" set of allocations. Everywhere else, something got in the way. In San Francisco, to take one example, channel 13 was allocated to Stockton back when KOVR was straddling that market and Sacramento, and when they finally moved east to secure a network affiliation with ABC, the allocation "officially" moved out of S.F.
Chicago couldn't use 13 either, because its assignment to Rockford was too close and had existed there as a channel 12 allocation since the original 1945 table. Since that was its lone allocation and 12 was too close to 11 in Chicago, Rockford got 13 (although in the 1949 proposal, it was replaced by two UHF channels, then was put back in 1951).
There were lots of such exceptions, which is also why UHF became a necessity for television service to get to most of America.