If the flow transmitter is installed in the field not reading correctly rather when calibrate in the workshop that is 100% accurate what's going wrong?

The nature of such flow transmitter problems strongly depend on type of the transmitter and its principle of operation. But generally speaking as Mr. Toufeeq quoted, and as my answer to this question the following items could be some of the reasons of this difference in the measurements:

1. Effect of difference between the process fluid characteristics and the test fluid characteristics used for the calibration (e.g different viscosity, specific gravity, ,,,) which has not been considered during the calibration.
2. Effect of elevation and suppression caused by the installation position and hook up devices which has not been calculated and considered in the calibration (specially for DP type flow transmitters).
3. Difference between the process condition (temp, press, ...) and the conditions in the calib. shop.

I believe to get more precise answer the question should be more specific.

Yes i am agreed to Mr. Danial Ghasempour.

Sometime it happen formation of air/bubble pocket which does not allow transmitter to behave properly. ..We need to flush transmitter and check LP and HP reading at location itself. ...

 Dear Mr. Danial Ghasempour thank you so much for your precise suggestions,  the characteristics  of process fluid (Damin water) and the test fluid (Damin water) used for the calibration is same (viscosity, specific gravity,)  because the flow transmitter is installed at the downstream side of the HP feed pump but the temperature is different.

so can you please know me something about temp effect ?