The final act makes absolutely no sense at all. Colonel Vautrain's plot to assassinate General Grant at Vicksburg is foiled when a cannon shell smashes into his mansion (where he was laying a trap for Grant), crushing his legs and detonating his cache of explosives prematurely. That cannon shot didn't happen in the original Battle of Vicksburg (since Grant used his house as a base and it's still standing in the present), and nothing he, West, or Gordon did caused it, so apparently history just spontaneously altered itself specifically to screw with this one guy. Then, when West and Gordon escape back into the present, they return to find Vautrain's mansion on fire. Why? If it was destroyed by an explosion in 1863, shouldn't they return to find a bombed out ruin? Has it been burning for the better part of a decade? Did Vautrain's daughter set it for some reason? It's like the writers just decided that adding Time Travel to the plot gave them a license to toss out all semblance of logic or cause and effect in writing the ending.
The earlier time travel bit makes no sense either. How does time travel account for Gordon apparently becoming someone named Jack Maitland, losing all memory of his true identity? How does returning to the present bring him back to life? Was it all some kind of illusion on Vautrain's part? Just how many incredible mental powers does this guy have??
I think the first time was a parallel/alternate universe rather than time travel.
What's going on in the poker game at the end of "The Night of the Running Death"? First off, the fact that Artie is losing so badly seems out of character for him, but are we actually supposed to assume that Jim is cheating somehow (which is hinted at, but seems equally out of character)? Secondly, is Artie's flipping of the table supposed to be some kind of attempt at cheating on his part, as Jim's reaction seems to indicate? That makes no sense - the table is specially rigged to keep everything on its surface(s) in place even when turned upside-down, as Artie well knows. Are we supposed to assume he just forgot? Thirdly, why does Artie get such a big grin on his face when he looks at his new hand, and why does Jim then start looking between Artie and his own cards in apparent dismay? Did Artie pick up an unbeatable hand and decide not to even bother bluffing anymore? How did Jim know it wasn't a bluff? All very odd.
It seems to have been written with filling up time before the last freeze-frame as more of a concern than story sense, as the episode was running short (the scene where Artie tries cherries jubilee with molasses and loves it has "tag" written all over it).
How does their telegraph receive messages in a moving train?