In general, he just doesn't like ALW's music, and doesn't mind saying so. But specifically, there's a section of Webber's Phantom of the Opera that bears a marked similarity to a part of "Echoes." The opening notes to the "Overture" of 'Phantom' (Track 2, Disc 1) are C# C B Bb A C#. This matches rather closely a section of "Echoes," approximately 6:06 to 6:16.
While Waters was less than pleased with this similarity, it has been pointed out that such a chromatic pattern is fairly common; by no means a Floyd invention.