Occured on 0.17.5, with SmarterTrains 4.0.1 installed. (I refuel with the bulk rail loader (mod)). Also i just use a generic station called "Refuel"

It should be fixed in the latest release. That being said, it worked for me with 4.0.1
My guess is that the first station in the schedule was far enough from the refuel station so that by the time SmartTrains checked if the refuel station can be removed (when arriving at a station), the fuel was below the upper amount?
Anyways, the refuel station should now get removed right after the train leaves the refueling station (that code existed for more than 2 years, but never got executed due to a mistake :D ).

Holy crap, thanks for the quick update. I'll try it later and tell you if it works for me :-D

Alright, in the one test case i tried it, it worked (same case it didn't work yesterday). A small other problem is, that when i use a personal train and ctrl-click to a location, the train drives there, but as soon as it gets there, it changes the Temporary waypoint to "invalid" and continues driving. This only happens, if it adds the refuel waypoint at the same time.

The new temporary waypoints/station are currently unsupported. Meaning i don't know what Smart Trains will do if you add them at a certain time. Trains assigned to a line might just remove them right away. I might find time to look into it on the weekend

still happens in V4.0.2 to me at least

Can you upload a save somewhere or provide a screenshot of the train schedule (where i can ideally see the refuel station, the first station in the schedule and the station before the refuel station on the map?)

you can join my server if you want ? its open but it has a lot of mods and you cant do anything until i promote you

Should be fixed in the latest update