All through the episode Tony calls the aliens 'Androids', yet when meeting Pete and Joan, he calls them aliens.
In the town, supposedly just about all of the residents are "frozen", yet many of them move.
During the storm near the end, the trees and bushes in the foreground are strongly swaying and blowing around, but those in the background are not moving at all. Also, the sky is bright blue, even though there is supposed to be a storm raging.
One lady that was "frozen" blinked.
The aliens are able to hide a small sabotage device inside the Time Tunnel computer - by the end of the episode though (the aliens are defeated by the oblivious Doug and Tony) the device isn't known about and found by General Kirk etc and removed from the computer.
When they encounter the rackmounted equipment, they mention how sophisticated it is. Tony then randomly throws a switch, complete with sound effect. It's unlikely that Tony, being an experienced scientist, would just throw a switch as though it were nothing.
When Tony and Doug first encounter Sarah Pettinghill, she mentions she has a batch of biscuits rising in the kitchen. Biscuits, being a quick bread, contain baking powder and do not need to rise like traditional yeast dough.