Just a guess here, but it sounds as if you may be having silvering issues. Silvering often occurs when you apply decals over a flat painted surface.
Flat painted surfaces appear to be smooth, but actually, the surface is covered in microscopic pits and irregularities. When a decal is applied, air is trapped under the decal and apears as whitish/silverish (hence the term) specks under the clear decal film. This is one of the most frequent problems which occur when applying decals.
The usual solution to this problem is to always apply decals to a gloss surface. Often, this entails applying a coat of clear gloss over the surface before decalling. There are also some decal setting solutions (eg. Gunze's Mr Mark Setter) which can help reduce silvering. The aforementioned Mr Mark Setter contains a mild adhesive which both fills in the surface irregularities in flat paint and sucks the decal down nice and tight - very helpful for decals which have been over-soaked or which have weak adhesive.
Then, if a flat final finish is required, a coat of clear flat will be required.