It's really just easily explain not as a drawing error, but the context of the drawing.
If the drawing is small (i.e. a very tiny panel), then why bother drawing the tome as it'll be too much work. When the panel is larger and the angles of the eye allow for it (i.e. squinting), then there are more tome in his eyes. The more room you have to draw, the better you can create the tome that are in Sasuke's eyes. However, if the panel is small, then the details in it become very crowded and it is better to just not show the tome altogether even though they have not disappeared.
This is done in a lot of other mangas and even in their respective animes.