I never leave my magnetic cleaner in the tank, as hyperfocal says, snails go in there, or other stuff, and it will scratch. I also use a pad on the inside float (in the tank) and run my hand over the one on the outside before using.
The Coralife Quik Wipes are great for putting over the magnetic cleaners. They're thin enough not to cause a problem with the magnets.
Before you use any kind of scraper or cleaner on an acrylic tank, run your fingers over it to make sure it has no sharp edges or embedded sand. Plastic scrapers can get dents/nicks in them that will scratch the acrylic.