Surprisingly, things happen with transportation that aren't planned. Breakdowns, accidents, traffic, shift changes, many things can affect when a bus arrives. One that is supposed to be there at a certain time many times, just isn't. No amount of planning can avoid this from happening. It's the nature of the beast and Disney is not immune from it. The only thing that you can depend on with public transportation is that they are only dependable within certain parameters and certain perfect conditions, which is how the arrival times are figured.
The last bus that went through, lets say WL will, in all likelihood not return again for quite a while or even the same day. The runs are shuffled to help prevent one area from continuously having late buses. If they didn't and the bus, for whatever reason, got delayed 20 minutes, it would stay that way all day long. It can never catch up because the times are based on research on how long it takes to get from point A to point B. That is constant. So a bus that ran from WL to MK, will probably not return to WL at least not right away. However, a bus that just loaded at POP and went to Epcot, may be the next bus you see at WL. If that one didn't get delayed then you will see them on time, if it did, it could be any amount late. There is no real purpose in posting arrival times, beyond every half hour or something like that, then it is arbitrary and is there when it arrives, not when you think it will.
I know that seems counter-productive but trust me, it is one of the best ways to insure that if a bus is late, the next one has a good chance of arriving when it should.