This could have several factors to contribute to the pin-holes of your coating on the substrates such as the concentration of your solution, the surface treatments of your substrates, the speed of your substrates during the coating. If you could adjust the mentioned factors, you should be able to overcome the pin-holes of your coating on the substrates.
effective cleaning of surfaces is an extreemly dificult topic, as Alan F Rawle correctly comments. And looking at this adsorbed films and its wetting/de-wetting is a tool for seeing these issues. For atomic force microscopy (AFM), we studied this in more detal here:
In situ characterization of nanoscale contaminations adsorbed in air using atomic force microscopy
Beilstein Journal of Nanotechnology 9(1):2925-2935; DOI:10.3762/bjnano.9.271
Thanks for your most valuable comments here @ Xuhua Wang, Alan F Rawle and Jamie Colchero. Appreciated.First, i tried different cleaning procedure (won't work), 2. I tried on changing the concentration within reagents ( these defects reduced but not well enough). The prime problem is organic solvent evaporation at ambient conditions. So I decided to add a chelate agent to control the reaction between intramolecular interaction. It paired with glass substrate by Hydrogen receiver as well as donor. Therefore, uniform coating with a internal gaseous stabilisation makes work finally.