On the DVD, in Kootie Pie Rocks, Milli Vanilli are clearly singing during their performances but no voices come out of their mouths (their music was replaced with a generic instrumental tune for legal reasons, and the "singing" clearly wasn't taken into consideration.)
In Mush Rumors, Kootie Pie is upset that when the "aliens" arrive, she doesn't have a thing to wear, even though she (like the other Koopas) doesn't wear clothes.
In Kootie Pie Rocks, Kootie Pie says she is going to change when Milli Vanilli are taken to the Koopa Castle, even though she doesn't wear clothes.
In 7 Continents For 7 Koopas, the views on Bowser's Doom Ship monitors change between shots. In one shot Princess Toadstool has her bathing suit on, in the next her standard pink dress, and in the next nothing can be seen on the monitors.
In 7 Continents for 7 Koopas, when Toadstool steals one of the Koopa Kids' wands, she can be seen with a sleeve on her arm. This doesn't make sense, since she's wearing a bathing suit for the episode's duration.
In Reptiles in the Rose Garden, Kootie Pie is flattened by the White House. In the very next frame she's NOT underneath it and shows no signs of being flattened.
In Reptiles in the Rose Garden, there are numerous positional inaccuracies with the Washington DC landmarks.
In Kootie Pie Rocks, the "NOW PRESENTING MILLI VANILLI" sign at the stadium misspells "presenting" (as "preseting.")
The Koopa Kids are the victims of numerous animation errors/miscolorings/etc. For instance, in one scene in The Beauty of Kootie, Kootie Pie's skin color clearly switches back and forth numerous times in the same frame. Likewise, Kooky was once drawn with green hands. Errors like this are extremely common, throughout the series.
In the Ninja Koopas episode, the Parrot's body is alternately red/green between shots. Sometimes its body is any mix of the two colors.
On the DVD, lots of the "remade popular" music was replaced with the generic "Mega Move" tune for copyright reasons. However, in Kootie Pie Rocks, this creates continuity errors. For instance, the first song they play is "Blame It On The Rain." Since it was replaced with the generic instrumental tune, Bowser's joke "Blame it on King Koopa" no longer makes sense.