Are you asking if it is possible or are you experiencing the problem. Acrylic tanks scratch easily. As ToeJam mentioned there is a differance in the magnet cleaners used on glass and acrylic tanks. Mag-Float makes both, eg. Mag-Float 130 and Mag-Float 125 are the same size magnet for the same size tanks yet one is for acrylic and the other is for glass.
Bushtech