In the Season 5 episode In Purgatory's Shadow (1997), Kira tells Jadzia that Kirayoshi spent seven months in her belly; however, in this episode she tells Odo that she had him inside of her for five months.
When older Molly is transported out of the portal, her hair is long and ragged, but during the close-up on her bracelet, it can be seen that her fingernails are neatly trimmed. This is unlikely, given her wild, back-to-nature existence.
The fruit that Molly and Miles eat never have any bites taken out.
When teenage Molly is retrieved from the past, she is still wearing the clothes that 8 year old Molly had been wearing before her disappearance. The two actresses are of too different body types for the same clothing to fit both of them, even tattered as the clothes are by her teenage years.
Teenage wild-woman Molly has bangs and is clearly wearing makeup.
In the Star Trek universe at least, going back in time will alter future history. At the end of this episode, teenage Molly goes back in time to a point just after little Molly arrived, and teen Molly helps little Molly come forward into the future. History is changed by this act, so naturally teen Molly ceases to exist, since little Molly now never got stranded in the past to grow up as a teen there. However, since history has now changed and teen Molly never existed, Miles and Keiko (and everyone else on DS9) would not remember or know of this episode's story. The only one who would remember teen Molly would be little Molly the time traveler. That would be consistent with all other time travel episodes in Star Trek.
When Miles and Keiko are discussing their plan to take Molly back to Golana, when Miles speaks the line, "Because there's going to be consequences," the movement of his mouth does not match the audio.
Worf coyly refuses to tell Dax what Yoshi's chant of "gung, gung, gung" refers to. If it is, as Worf earlier claimed, a standard Klingon game, it would be strange that Dax, an expert on Klingon culture, would be unaware of it. Worf himself would have had to have found out somehow through study, as he did not grow up in Klingon culture.
When Miles walks in on Molly's freak-out, Keiko says "She's been like this for over an hour." If Molly has been this disturbed for that long, it does not make sense that Keiko wouldn't have called someone, especially Miles or Julian.
During Molly's freak-out, Keiko says she needs to go pick up Yoshi and bring him home. Yoshi was just seen dropped of in the O'Briens's quarters by Worf.