My observation is that the bad habits are often taught (or allowed to form) in the sausage factory schools purporting to be airline academies... However, I note this is more a function of the individual instructor than the school in probably most cases - the big schools tend to be inundated with very low time instructors who are ignorant of the training standards required and simply chop through a syllabus
Now there is someone who knows what he is talking about. The low time instructor only knows what he was taught by his instructor and the process is repeated down the line from instructor to instructor. There are exceptions of course but it's a good bet the average CFI of a big school probably hasn't a clue of the real standard of every instructor under him since it is below his status to regularly fly with ab-initio students as a quality assurance check.