After B'Elanna changes the Doctor's family, the wife's hair becomes short and "modern," but later it is long once again, even though the Doctor hasn't asked the computer to alter the program. The change of the wife's hairdo is, however, less the result of B'Elanna's or the Doctor's programming than the personal choice of that holocharacter, who (given the nature of the holo-program) has been given a certain autonomy over her actions and preferences.
When B'Elanna freezes the Doctor's Holodeck, the fire in the fireplace continues to burn.
After the Doctor scanned Belle and determined she had "died", the camera showed, as Charlene is starting to sob at the loss of her daughter, Belles' eye on her right side open and close. Also her head twitches.
Having dinner with the Doctor and his family, B'Elanna seems to satisfy any hunger she may have from the meal. In other episodes, the crew has to save energy and ration to use food replicators or else suffer the cuisine of Neelix. If the crew can freely use the holodeck, they could easily have scenarios where they get well fed and bypass the replicator rations. Also, if the ship has to ration their energy (assuming the replicators use the same energy source as the holodeck), why do they make such frivolous use of the holodeck? Furthermore, why does a utility hologram appliance such as the Doctor even need to use the holodeck, wasting more ship's energy?