From the mathematical point of view, there's no doubt: squares (quadrados) are a special case of rectangles (retângulos), and any teaching material saying otherwise is in error. That's not dependent on the dialect.
That said, in informal or any other less precise speech (which should not be used when teaching or discussing mathematics), one may mean "typical rectangle" when saying "rectangle", excluding therefore special cases such as the square, as well as degenerate cases, such as a segment of a line (i.e., a rectangle with a side of length zero).
A similar situation arises when discussing ellipses and circles, as the latter is a particular case of the former; and humans and animals, where the latter might implicitly not include the former.