Why warning letter was issued and what were the charges? What is the nature of miscondut? you have not briefed it. Is the warning issued is for late coming , frequent unplanned leaves, is it for performance related issues. It depends. If the warning is performance related issues or any other major misconduct then the Company reserves the right to delay or hold increment for the particular employee.
During annual appraisal apart from performance all other criteria like punctuality, leave availed particulars, number of warning issued during the period under review... all will be considered.
But it depends on the field IT and non IT differ. IT, ITES, BPO offer flexible work hours, people stretch and work and come late in the morning... so definition of punctuality is different there and whether work assigned is completed within the stipulated time frame is counted there. In non IT it is other way.