I am attempting to combine my favorite aspects of the 3d icons which various people have modded over the years; specifically the 3d,4d,5d set which holds the minefield signs, armor wrecks and objective symbols etc. XMGO had a set with my favorite wrecks and I want to cut and paste swastika/sickle objectives from another set thus combining the two into one mod. When I do this, I get "ragged" white edges around the objective symbols in the game display. Is magenta the color I would use to clean up the jaggedness. I'm not a graphics guy but I am willing to learn!
What you describe there is likely caused by anti-aliasing creating "soft edges", which happens when scaling graphics up or down, unless using a scaling algorithm that specifically does not use anti-aliasing. You'd need sharp edges, where the background color (magenta, in most cases) and the unit shape have a clear border.
So either, if you have the original file and need to resize it to smaller sizes: use a resize algorithm that does not use anti-aliasig. In PSP it's the Pixel Resize option, and with GIMP it is Interpolation: None.
Or: if you already have the graphics files where anti-aliasing took place, you'd need to manually tidy the shape edges. It could be a lot of work. So in this case, if this is an issue with most tiles, I'd say resize from 3d manually using a non-anti-aliasing (is that a word?) algorithm.
Hope this helps! If not, ask again, I'm happy to help you out with this.