Did you rush the tempura? In a word, maybe…
All coatings, clear included, tend to be drawn into corners of any kind, leaving a thicker layer in and near those areas. This is a result of surface tension, and there is no way to prevent it.
As a result, the coating in and near panel lines is thicker than elsewhere. It takes longer to dry and longer to cure. What often happens is that after the surface is dried and cured, the coating below the surface still contains small amounts of solvent. This solvent migrates away from the panel line (where the coating is thickest) to the thinner areas at some distance from the panel edge. Where the solvent finally migrates out of the coating, the coating is softer and uncured for nearly as long as the heavier coating at the panel line. It can take up to twice as long for such areas to dry and cure compared to the middle of the panel. Applying your wash to this slightly sticky or possibly faintly rougher surface resulted in pigment being trapped there.
It sounds from your description that this is what has happened. This is a common problem in all paint applications, not just scale modeling, and it is worst when a heavy coat is applied, instead of multiple light coats.
You may be able to remove the stains by polishing the surface with 2000 or finer grit.