Dear Gurunathan Selvakumar, most probably that these small black spots found on your samples appear perhaps due to enzymes activity. I suppose, that these spots indicate the initial stage of starch hydrolysis/ degradation caused by alfa-amylase.

However, to be enough sure could you describe storage conditions more detailed

Sincerely,

Vitalijs

although I'm not sure about the storage conditions

I agree with the explanation of Vitalijs Radenkovs that amylase action could be a plausible cause, especially if the spots are really pores. I recommend 2 experiments to get more clarity on this.

1. Investigate the development of pores at different storage conditions (storage time, temperature, and humidity)

2. Perform an amylase activity assay on the starch granules. 

Both two respondents are right. However the answer is difficult because (as Vitalijs mentioned)we know too little.

Thanks for your valuable answers, I found that Alpha amylase activity is more in this flour sample. My doubt is  "How to call that dark appearances while writing research paper". Kindly suggest me. 

Formation of deep pores is typical for cereal starches when hydrolysed in their granular form. Please look at Fig. 2 in the attached paper. Probably you can see the initial/current stage of hydrolysis.

You could describe your observation as: 'The dark spots suggest the initiation of  pitting, i.e. the formation of small pores by amylase action'. To strengthen the evidence for enzymatic attack it is recommended to present micrographs at different incubation time and/or to analyse your sample for the presence of reducing sugars.   

Thank you very much sir...