While probably a simple writing blunder, Harry's mention of golfing against Ensign Kaplan to Steth/Tom is probably one of the most serendipitous blunders in all of television. Harry is talking with someone impersonating his best friend, four years into a journey where the whole crew has long since gotten used to hazards like alien impostors. Harry in particular is clearly no longer the naïve dweeb he was in Season 1 by this point. Harry probably sensed something was off about his best friend, and decided to toss in a dead shipmate's name to see how or if "Tom" would react. Had the conversation gone on a bit longer, Harry might also have said something like "and after that, don't forget our double-date with Kes and Seska."
Some fans have questioned whether B'Elanna slept with Steth thinking he was Tom, in which case she would technically have been raped (at least by the current definition of the word). And even if fraudulent sex isn't considered rape per se by the 24th Century, it would still be an incredibly creepy thing for poor B'Elanna to realize after the truth comes out. To say nothing of what kind of alien diseases Steth could have been carrying.
Some of the shapeshifter's victims might be dead. That means not everyone will be reunited with their original bodies and some will be stuck being another person forever.
Even worse, some of the dead ones might have had their names permanently sullied, and loved ones forever thinking terrible things about them.
