All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad is His slave and Messenger.
The employee has to abide by the contract and its terms and regulations because Allah Almighty Says (what means): {O you who have believed, fulfill [all] contracts.} [Quran 5:1] Also, a Prophetic Hadeeth reads: "Muslims should fulfil their conditions (in contracts)." [Abu Daawood and classified as authentic by As-Suyooti].
The fact that some employees do not abide by this does not allow others to breach the limits agreed in the contract. This matter should be verified by referring to the employer and asking him about those procedures, and whether or not they mandate that employees must follow them? This is the employer's right, and if he agrees to make a concession, then there is nothing wrong in it.
Allah knows best.