When Wanda is listening to Molly Cule's "Down to the Very Last Bit" in the opening scene, Dorothy Ann can be heard singing her line. The kids don't join in the song until the end.
If the kids shrink so much that they are able to see soap and water molecules, the air around them should be a mixture of molecules as well.
During Molly Cule's concert at the start of the show, when the camera pans to Ms. Frizzle's class in close-up the second Molly Cule greets the crowd in attendance, the sleeves on Phoebe's shirt are miscolored red like her shortalls, but the yellow collar to her shirt is visible during this camera angle.