The blue blotches are most likely caused by the film making surface contact with the scanner glass or another surface. The film holder normally prevents this by keeping the negative slightly raised, with space above and below it.

If you want to include the sprocket holes, try raising the film off the glass without covering the edges. A simple way is to place thin strips of cardboard on either side of the film strip as spacers. That helps avoid direct contact while still leaving the sprockets visible in the scan.

In short: the issue is physical contact, not the scanning software. Keeping the film slightly elevated should eliminate the blotches.