I think it just happens now and then.
I wrote in my recent trip report about our experience in July.
We jumped on the Railroad as we were leaving the park about 10pm or so. I thought we could have a quick loop around and be back where we started at Main St Station and then head out, none the worse for wear (my husband has issues walking too much)
We came to a stop around the back near a SW:GE entrance, a little way out from the Toon Town Station.
Not sure which train we were on or the one in front but the one ahead of us at TT had broken down. We were stuck for about 40mins while they decided what to do.
Eventually they backed the train up that was behind us back to Main St and then we backed up to NOS.
We were then left having to walk all the way back to the front entrance from NOS - husband not happy!
According to the app the train was down the next morning but was up again by lunchtime / the afternoon as we rode it then.
Like any of the attractions I think they just break down every now and then - it happens : )