As others have mentioned, make sure that you aren't getting coralline algae trapped in between the magnet and the glass. I would suggest rinsing it before and after you use it to get rid of anything that may be scratching the glass. There are other things, such as calcium carbonate precipitate or even detritus, that could be causing scratches as well.
Calcium carbonate is definitely hard enough to scratch glass. Most reef sand is aragonite (a form of calcium carbonate), so it should be fairly obvious that coralline algae and snail shells would have the ability to do so as well - they are made of calcium carbonate after all.
For glass, I suggest using razorblades personally. Just make sure to rinse them with freshwater afterward (to prevent corrosion) and then dry them with a towel (or just shake them off) and store them away from the tank (to prevent corrosion from salt spray/creep) as well as any small children that might be looking for a shiny new "toy" :lol: . Razorblades are relatively cheap (we buy them in bulk in my lab for less than 10 cents a piece), so replacing them when they get worn isn't an issue. If you don't want to be wasteful (like me) then you could just buy a sharpening tool to keep the edge sharp. I use the "v"-shaped wedge type sharpener just to make sure I get a good, clean edge.
For acrylic, I would suggest using the Kent Pro Scrapers (red plastic blade with the black handle). I've tried rigging up my own scrapers, but they always end up breaking or scratching too easily.
If you don't want to get your hands wet, then I believe they sell razorblade attachments for magnet cleaners. I've never tried them personally, but I've always wanted to.
For cleaning coralline algae on acrylic, I'll actually use an electric tooth brush ($10 Crest Spin-brush Pro - to be precise). It takes it right off with no manual scrubbing required. You could use a regular tooth brush as well, but where is the fun in that?
