Maia's sister Sarah shows up and abducted at minimum 5 children. Including Maia, Tyler Downing, and Lindsey Hammond and 2 others. It was later revealed that Maia sister was actually someone trying to repair the time-line and was sending these children further back in time to try to fix the future. This being a time altering even we see the objects around that were directly related to Maia being present in the time-line all vanished and everyone forgot about her existence. When this happened.. At least for the duration of the episode... Every mention of the 4400 should have been changed to the 4395 because those 5 children would have not came back during the initial return.
When Tom was driving and hit the child, many skid-marks were present on the pavement. Yet afterwards the overhead shot reveled there were no skid-marks.
A 4400 remarks that he can smell pheremones. He matches people up that smell 'the same'. Pheremones act as emotional stimuli and carry an array of markers that can identify a particular human's major histocompatibility complex (MHC). Current research supports the notion that MHC acts as a genetic marker of relatedness that prevents inbreeding and thus the exposure of deleterious allele combinations. Thus, an ideal match would be a person who smells 'different', not the same.
If the children had never been left with the other returnees then they would have been the '4395' not the '4400'.