While the Time Tunnel scientists instruct David to jam the bomb's dial with one of the tools, all subsequent shots of the bomb upon returning to 1861 show the screwdriver David used merely sticking out of the side of the bomb, quite far away from the dial.
The tools that Kirk threw to David in the Time Tunnel should have been sent back to the depot with him and bomb (as they were also in the tunnel), but only the screwdriver David used to disable the bomb was shown as David reappeared in his own time.
From watching this episode, it appears that you could count the total population of the city of Baltimore in 1861 on your fingers. No-one is seen in the city streets apart from the plotter brothers, the Pinkerton men and Doug & Tony.
The layout of the bomb, the depot, and the train (and how Tony throws the bomb away) doesn't seem to make much sense. The bomb appears to have landed on the other side of the train from the depot, but there is no indication Tony threw it that far, or past the train earlier.
When the (stock footage of the) train pulls out, there is no sign of the depot or any buildings whatsoever.
The Pinkerton men fail to see the rather extensive brawl that Doug and Jeremiah have pretty close to the train as it departs near the end of the episode.
When Jeremiah and Matthew talk outside the depot about two-thirds through the episode, the voice sync on actor Scott Marlowe is not very well done. Particularly when he says, "No, no, no", his lips don't move at all, or fail to synchronize very closely with the on-screen dialogue.
Although the hints that the Time Tunnel has "forged its own connection" are intriguing, there's no real explanation for why the Project staff witness Lincoln's assassination in '61 at the beginning of the episode.
Lincoln: Slavery is an evil that men of reason will eliminate, with reason.