It is not a bug, although I can imagine an argument for changing the bahaviour (although not precisely in the manner your stated).
The intention is that you can design a timetable for a line in which a number of trains follow the route of the line at regular intervals, with this spacing being controlled at some of the stops (those with "Wait for time" selected). If the spacing intervals were set to different values at different stations, then eventually those stations with a smaller spacing interval would run out of trains that are ready to depart at the specified interval (because a station with a larger spacing interval would not be sending trains quickly enough). This does not fit the original design, and thus is not permitted in the schedule gui.
However, I can envisage a scenario in which having different frequencies at different points in the line would be useful. Consider two passenger services (using separate tracks) running at frequencies of 5 trains per month and 6 trains per month. We now want to add a freight service that shares parts of the railway that these two passenger services use. To avoid disrupting the passenger services, we want to fit the freight service into the gaps between passenger trains. We could do this for the first service by setting a timetable to run at a frequency of 5 trains per month, offset from the timetable that the passenger trains are running to at that point. This timetable doesn't reflect when we expect trains to run every time, but rather a set of slots in which the freight trains are allowed to run. However, we cannot then do the same thing for when the freight service uses track that is also used by the second passenger service, because that is running to a different frequency.
If you are wishing to do something like the scenario I just described, then I think the way to enable this should be to add a second tickbox to the gui that allows setting a different number of slots per month for different parts of the route. Another useful option could then be the maximum time by which a train could be late for its slot before it is assigned to the following slot instead. So for a freight service using gaps in a passenger line that permitted lateness would probably be 0, but for a scheduled bus service it should probably be considerably higher (maybe half of the interval between busses, or the entire interval between busses).
Oh, which reminds me: I think it might also be useful to have an option to aim for a specific departure slot relative to the departure slot from the previous wait point. This would help to avoid situations like a shipping line where the interval between ships is less than the loading time, and the ships end up departing late for an earlier-than-intended departure slot at one of the line, and then waiting ages at the other end.
