In Tempus Fugitive, Clark built a second time machine with the help of HG Wells' plans. By the end of the episode, there were two time machines in Smallville, one at Rocky Cove, one in the alleyway next to the Frozen Foods store.
Wells used the first time machine, the one he built, to take Tempus back to 1866, and told Lois and Clark to meet him at the second time machine. Then he took L&C back to Metropolis using the second time machine built by Clark.
This means that one time machine (the one built by Wells) stayed behind in Smallville in 1966. Correct?