Ok, so it sounds like you're using ChannelFly to dynamically assign channels. ChannelFly is a statistical analysis algorithm based off actual observations of throughput on your network, not based off conventional heuristics (such as assign adjacent AP's non-overlapping channels).
In my opinion while it has its limitations and caveats, it does tend to be quite effective, especially in the real world where rogue AP's and other external circumstances generate 2.4GHz interference outside your control.
I'd recommend dumping the support info for your AP's to inspect the historical channel capacity statistics, to see if you agree with ChannelFly's observed throughputs on other channels. It might not be as disadvantageous as you might think for adjacent AP's to use the same channel, if the load is light and the other channels have even worse throughput.
The ChannelFly algorithm always chooses the channel with the highest observed throughput potential.