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It looks like the pump otherwise functions correctly -- animations require the fluid wagon to be aligned with its new position and such.
The issue can likely be reproduced with no mods using just a console command -- but as I'm on my phone at the moment I can't look up the specifics. To my knowledge it can't happen in normal vanilla gameplay as that doesn't have any entity teleporting mechanics. Will have more information tomorrow if this isn't enough to go on.Added support to teleport train stops, rail signals, walls, gates, and entities with fluidboxes.