In VeggieTales: The Star of Christmas (2002), the stained glass in St. Bart's church was very simple, abstract shapes. In this film, however, the glass becomes a central part of the plot, and is shown to be very ornate portraits. However, some time has passed between the two films. It's possible that the church has had its windows replaced since the first film, especially considering that it has a new round window.
As the egg container flies past Bob and Larry (having a conversation)once collecting eggs along the way, during the end of their talk eggs pop out but aren't collected from the container, they just disappear in mid air.