Does sin accrue to an employee who carries out unjust deduction decisions against workers, even though he knows of their injustice and sometimes tries to remove them?

What you have mentioned does not necessarily have to be entirely unjust. Some of it is based on work systems, regulations, and conditions agreed upon between the worker and the company, such as deducting days from a worker for going on Hajj, or penalizing him by deducting two days for speeding. If these matters are part of the agreed-upon work regulations, then they are not considered injustice. If they are not part of the regulations, then they are injustice. There is no blame upon you for the work mentioned, but it is not permissible for you to carry out any command that involves injustice; due to the Almighty's saying: "And do not cooperate in sin and aggression."