Form 16 is the annual TDS certificate an employer issues under Section 203 of the Income-tax Act for tax deducted on salary. It has two parts with very different provenance. Part A is generated by the employer from the TRACES portal — it is effectively a printout of the department's own record of tax deducted and deposited against your PAN, quarter by quarter, tied to the employer's TAN and the TDS returns (Form 24Q) they filed. Because it comes straight from TRACES, Part A numbers should already agree with your Form 26AS / Annual Information Statement (AIS) for that employer.
Part B is different — it is the employer's own computation, prepared (not government-generated) to show how gross salary was reduced to taxable income: gross salary under Section 17(1), perquisites under 17(2), profits in lieu of salary under 17(3), Section 10 exemptions the employer processed (like HRA), the standard deduction, any Chapter VI-A deductions claimed through payroll, and finally tax computed under whichever regime the employer used for TDS. Because Part B is prepared by the employer based on what you declared, it is the part worth checking line by line against your own records — Part A is largely just confirming what the department already has on file.
Employers must issue Form 16 by 15 June following the financial year. If a return is filed using Form 16 numbers that don't match 26AS/AIS, the usual first step is confirming whether the TDS was actually deposited and reported (a Part A / 26AS issue on the employer's side) versus a computation difference in Part B (a discussion with payroll about what was declared and processed).
