Transit uses the MBTA API to retrieve data about the schedule and about where buses are currently. They provide this guide to determining whether the data you see is based on a schedule or realtime data https://help.transitapp.com/article/445-how-to-track-departures-on-your-transit-line. If the realtime data you see is off/flaky, it’s the MBTAs fault because the data is taken from the MBTA API. If the ghost buses are based on schedule time data and not realtime data, that means the bus is either delayed relative to the schedule or that run was cancelled by the MBTA (and not reported as such on the API). I recommend only looking at realtime data for the buses unless you’re near the beginning and end of the route since realtime data is typically much more accurate (but often realtime data only starts reporting once the bus leaves its origin stop)