The answer lies in the synthesis process itself. For eg synthesis using conventional solid state route may introduce a temperature gradient which will effect sintered surface and hence particle size and shapes. Similar observations could be observed by changing the ball to powder ratio during ball milling and so on. Similarly you could think about the process used by you or if you find it appropriate I suggest sharing the process and material details so that experts in the field could provide better explanation. Hope this will help. 

First, what is the material and what were the reactants being using for synthesis? Synthesis conditions? Experimental set up?

Answer these and you could find there is a chance that you are actually synthesizing more than one  material. In some cases you could be synthesizing the expected material as well as an oxide or nitride or etc.

The answer above is also possible as temperature CAN greatly impact crystal morphology (even if it is the same material with the same composition).

thank you guys for taking interest,

I have synthesised Pd nanoparticle wrapped with garphene oxide, reducing agent used here is GPTMS. 

Yes, Agree with Gaurav and Kirby. Pd NPs are not fully formed means it depends on the temperature, reducing agent, anisotropic effect,