I often begin a turn by checking arrivals, moving these, bringing units from reserve to the map, doing any strategic movement by rail from one part of the map to another, repairing rail, creating depots etc. All the "admin" tasks before concentrating on combat units. I noticed that if I enter Rail mode to move say a new division from near Berlin then go to a Rail Repair unit, it treats the Rail Repair unit as if it on a train, and you can't move it forward to the next hex to continue repair of course. But the problem is if you then click back into normal movement mode it seems to treat the Rail Repair unit as just having been unloaded from a train, even when it never actually went anywhere by train. And so all of its movement points/rail repair capacity disappears for that turn.
It's possible that this bug occurs with other units when you have Rail mode enabled and select them, then change to normal movement. I haven't tested that. But that is not so annoying as losing the ability to carry out the very scarce rail repair capacity, when you are trying to get freight forward in the early stages of the game (advancing as Axis).
I thought something like this might have happened a previous turn when I came across a Rail Repair unit which appeared to be loaded onto a train and I had to "unload" it. When it happened again, IO thought I was going crazy as I was sure it had not been on a train the previous turn. I went back to the Save game and checked that it definitely was not loaded onto a train and then realised that it was because I had had Rail mode enabled from the strategic movements when I selected the rail unit. No unit should be counted as loaded onto a train just by entering the rail mode, nor even when rail mode is enabled and no rail movement actually takes place. Because this clearly does not account for accidentally entering rail mode, or accidentally selecting a unit when in rail mode.
Edit: This definitely occurs with other units too. As soon as you have a unit selected in Rail mode and click anywhere on the map, even in a hex which has no rail (which is what happened with the Rail Repair) you hear audio of a train, and the unit is then locked into rail movement even though it hasn't gone anywhere by train. When you then choose normal movement mode a combat unit is treated as being unloaded (it passes the Strategic Movement Points test because it hasn't used any of the 200 it gets) and can typically still move, but has only a fraction of its MP left. Which is probably why it hasn't been noticed before. The impact is much greater if you are genuinely moving units by rail and the very next unit you select is Rail Repair. Fair enough if you did actually want to strategically move a Rail unit by rail to another part of the map, but not when you just want to advance to the next hex along a track.
Since there is no explicit Load on to train button, but an implicit load by being in Rail movement mode and actually moving, then that should check that the unit really did move somewhere, ie. that at least some of the SMPs were used up. If you are still at 200 SMPs then you should be able to change to normal movement mode with no penalty and your full MPs available.