If two employees are paid the exact same amount, how come cpp and taxes are different?

Has it got anything to do with their TD1 or age or Year to Date Earnings?

These are the only real variables to CPP and Taxes

Your TD1 form allows you many different Tax allowances and while there is a "Standard" many people can have differences here which will always result in different Taxes

Age is an issue, people younger than 19 or older than 65 will not (usually) have any CPP deducted. Likewise changing to this age mid-year will result in differences in CPP

Lastly you have YTD Earnings, when someone maxes out their CPP for the Year they simply do not have to pay anymore. The Maximums can be found on the CRA Website.

Other than things like this, I really do not know why they could be different?

(Different Provinces or Status as an owner or relative not withstanding of course)