Is this an academic discourtesy? I co-wrote an original short paper with a senior colleague on the history of science. It was submitted some months ago, and was reviewed and rebutted several times before it was finally accepted and is now in print. Its topic is somewhat controversial. During the review process we had to battle to be allowed to 'air' our opinion about one particular issue. 
To our surprise, a few weeks ago the same editor (with whom we had engaged at length during the review process) then published a short article in the same journal, one quarter of which ALSO mentioned the original topic we had drawn attention to and had indeed battled over.   No mention at all of our original published work was made - even though we had published only a few weeks before, and we had had to negotiate in detail in terms of what we said about specific topics.  Is this an academic discourtesy? It feels somewhat dishonourable - especially since our work put forward an original, highly-relevant viewpoint and is very recent.
If I understand your question and comments correctly, the sequence of events is this:


The editor handles your paper at time X.
The editor submits their own paper, with a submission timestamp after X.
The editor does not cite you.


If this is the case, then the editor should certainly have been aware of your paper at the time that they submitted their own, and thus been able to cite you.

Failing to cite you thus seems likely to be a case of scientific dishonesty.  There are, however, certain circumstances where failure to cite might be acceptable, such as:


Other papers similar to yours are already cited (e.g., "phenomenon X has been noted a number of times, including [cite, cite, cite]")
You are somehow misinterpreting the date stamps


From what you've written, however, it seems unlikely that one of these cases applies, and more likely that you're dealing with a case of dishonesty.