Can you please post your complete project so that we all can have a look at all of your settings. To do so, use
Creator->File->Create Workspace Bundle (minimal)
and attach the resulting file.
Please check the attached file
i attached the project
Project compiles with errors.
Are you using a Cypress Kit (which one?) or your own PCB?
Check the stability of your 3.3V supply.
Could be better to change the ADC to "Hardware trigger" and using ADC_StartConvert() API to make a single conversion. StopConvert is not needed. A short delay to settle voltages could be helpful.
For later project stages (not the current issue):
Every global variable that is changed in an interrupt handler must be declared as volatile!