I have had negatives in archival sleeves made by Print File (the brand you link to) for decades. Just sitting in the sleeves will not cause scratches or produce residues.

Scratches

Scratches are created when a hard substance scrapes across the surface of the film. They can be formed in camera, during development, or when handling the film. Scratches may have been created when you "scrubbed" the negatives.

Residues

Residues may be left behind by adhesives, evaporating liquids, or degrading plastics.

It is unlikely that the material the sleeves are made from are degrading because the product you link to is of archival quality and stable. I have had negatives in sleeves produced by the same company for decades without any problems.

Degradation of plastics may be accelerated. For instance, the glycerin base of sunblocks and hand lotions can dissolve plastics, in addition to leaving their own residues.

Since you saw "water spots", it is likely that a liquid, such as juice, splashed onto the negatives and left a residue upon evaporation.

Prevention

• Wipe away dust from all work surfaces with a damp cloth followed by a dry cloth. Alternatively, a dry dusting cloth, designed to pick up dust without throwing it into the air, may be used.

• Also, wipe dust away from the binder and sleeves. Make sure your equipment and scanner are clean.

• Remove foods, drinks, and other liquids from the work area.

• Wash and dry hands before handling negatives. Avoid antibacterial soaps and "water resistant" skincare products. Do not put lotion on hands after washing.

• Make sure negatives and sleeves are clean before replacing negatives for storage.