Another confirmation here. Although I don't even have to wait for the first strike craft to build. I can queue up the max number, then dequeue them and go for the other type, and the maximum number of both kinds will be built (eventually).This happens for hangar defenses as well, but you have to make sure you do it after the hangar is finished building (you are allowed to queue strike craft beforehand, but it won't experience this bug in that case).
The reason for this is that when you queue in advance the fighters don't exist yet. So the queue order is cancelled, but there is no unit to scuttle.