Apart from the usual density/matter problems associated with science fiction shrinking, one additional problem is that anti-matter energy yield should not change, regardless of the compressed state of the matter. The annihilation of matter and the resultant energy would be the same, regardless of the size of the matter involved. Therefore, the photon torpedoes fired by the runabout when they were taking over the engine room should have still had the same yield as normal photon torpedoes, and would have blown the Defiant apart once fired at the Jem'Hadar in the engine room.
Worf states that the experiment will help with research in trans warp drive but the Excelsior in The Search for Spock has trans warp drive around a century earlier.
When the crew in the runabout finally are able to open the blast shutters, they look straight and up through the shuttle windows and see the Defiant. but when the picture zooms out, the Defiant is below the runabout, considering the angle of the runabout, all they should see is empty space.
Dr Bashir states that beaming compressed "shrunk" air into the compartment would supply the crew with about 20 minutes of breathable air. Near the end the crew are gasping for breath, but more compressed air could be beamed in at any time.
O'Brien demonstrates with his fingers the size he thinks their height has shrunk to, holding his forefinger and thumb 2 inches (5 centimeters) apart. Bashir corrects him saying "This much", holding his fingers 1 inch (2½ centimeters) apart. Throughout the episode, however, it is repeatedly stated that the height of the crew is "one centimeter" (less than a half-inch).