Such effects may be observed as the result of multiiple troubles, including poor quality of plastic surface, bad thawing/ freezing, or even contamination, Simply start from plastic (Nunc or Corning - best choice). If no change, check the other items.     

Hello Perumal

The problem you state is a handling problem in my experience. I agree with the suggestions of  Andrey and Sheikh. Additionally, it also depends on the type of cells you are using. If they are known to form clumps, its best to homogenize them through pipetting gently and repeatedly. You can verify if you undid the clumps on the neubauer chamber you use to count the cells. Some cells do this vortexing type centring and clumping upon exposure to 37 degrees Celsius, its almost funny but troublesome. What we do is to keep them at room temperature for 10min or so before putting them into the incubator. Depending on how quickly your cells adhere, you can also check your flasks a little while post subculturing to see if you already see the accumulation in the centre, if yes try shking the flask horizontally only in one direction (only slightly vigorously). Sometimes, it helps to scatter the cells, provided its not too long post adherence. Also, a not of caution if your cells are super sensitive....moving them too much is a bad idea then (like primary cells).

One last observation that we have seen with our cells (HepG2) is senesitivity to trypsinization. Over trypsinization can lead to increased clumping of the cells upon seeding. You may want to confirm that for your cell line.

Concerning if this will affect your cells, just a not that overcrowding of cells can lead to necrotic spots in the bulk, which may create some stress response in the neighboring clumped cells. This may skew your observation if you study the population. 

Hope this helps and good luck

Aparajita