Hi Ehasan
Agree with kschewe. This will be contaminants leeching out of the substrate and can be difficult to remove.
I understand the pressures bought to bear
(Since we were short of time (the job being carried out during Shutdown), but it is vitally important to get the substrate preparation stage as near to perfect as possible or you will be building your coating on an unsecured footing. Impossible to correct without starting from scratch.
This is not usually a problem with new builds, but repairs to surfaces that have seen service often have suffered pitting corrosion, which can contain contaminants. After, typical cleaning and grit blasting, these contaminants leech out staining the the freshly prepared surface. Problem here is that this may not become evident until some time has passed or when preheat is applied.
Plan in a extra time/materials for cleaning, heating, grit blasting for the preparation stages, you will probably need it.