Although most of the flashbacks in D.W.'s Perfect Wish are clips taken from older episodes (with the music replaced), the flashback to when Mr. Rogers is at their house actually features new animation of Mr. Rogers singing to D.W. as she is sleeping in bed (in the original episode, Arthur Meets Mister Rogers, he was singing the same song to Buster and D.W., whom was awake at the time).
In this show, DW turns 5. Presumably. But nothing changes. The following episode, she's still 4.
In "D.W.'s Perfect Wish", Arthur reminds D.W. of the time she got the chicken pox from him, and she says "That wasn't fun." Actually, D.W. was overjoyed when she came down with them because of all the special treatment. (Watch "Arthur's Chicken Pox")
Arthur: (in a fantasy sequence...) Uh, what's for breakfast?
Mrs. Read: (smiling) I don't know. Your father always made breakfast.
(Arthur and D.W. give odd looks)
D.W.: So there's no breakfast?
Mrs. Read: (giggles) No!
(knowing they will starve without Dad around to make the meals, Arthur pats his stomach as it growls loudly)
D.W.: You... you wear glasses!
D.W.: These were the memories of my childhood? A buck, a firedrill and a fatlip?!
Lullaby Arthur Sings to Kate: Go to sleep, go to sleep, you've been awake for so long now, count all the sheep, and subtract a cow, so you can go to sleep. (Pal Howls)
In D.W.'s flashback in which she asks Dad for a "normal cake," the cake he's decorating at the time features the words, "2 days ago," which he quickly covers with another decoration. Clever!
As D.W. talks to Arthur about how you're only four once, she holds up three fingers. Also, when Arthur tells her "no," she asks him if that's all she gets, a three-letter word.