Sometimes it was with a small number of units and would still happen. I think I saw it repro with double click and drawing.
Finally figured this, funny issue, the unit partially inherits character of "being an artifact" from an exhausted (destroyed) artifact, because specifically the cache keeping artifacts-per-coven was not cleaned up. So, like Artifacts, the unit then can not be included in group-selections. Issue did not come up before last week, because Artifacts used to have 5000 HP and not be consumed. Anyhow this caching was always near-useless and waiting to introduce bugs, guess I will get rid of it altogether.
So sometimes that coven would be at the max spawn but the yellow bar would keep scrolling.
The spawn progress goes on. If you managed to lose a unit in time and no longer be at max spawn when bar is full, the spawn would happen.