Praise be to Allah.
If an employee is entrusted with some work, then what he must do is fulfil that trust properly, because Allah says (interpretation of the meaning):
“Verily, Allaah commands that you should render back the trusts to those, to whom they are due”
And the Prophet (blessings and peace of Allah be upon him) said: “Allah loves, when one of you does something, for him to do it well.” Classed as saheeh by al-Albaani in Silsilah al-Ahaadeeth al-Saheehah, 1113.
Based on that, if this overlooking of specifications is something minor that is usually overlooked in contractors’ work, there is nothing wrong with overlooking it.
But if it is very different from what is required, to the extent that it may be regarded as deception or corruption, it is not permissible to accept the work from the contractor unless one writes a report of the shortcomings in which the contractor did not adhere to the specifications.
Even if in this case your boss instructs you to overlook it and accept the work, it is not permissible for you to obey him, because he is instructing you to deceive and lie, and the Prophet (blessings and peace of Allah be upon him) said: “There is no obedience to any created being if it involves disobedience to Allah, may He be glorified and exalted.” Narrated by Ahmad (1098); classed as saheeh by al-Albaani in Silsilah al-Ahaadeeth al-Saheehah, 197
If you can refer the matter to those responsible so that they may take appropriate measures, that will be a good thing. But if you are afraid that one of them may harm you, then it is sufficient to refuse to accept the work unless the faulty specifications are recorded. Then you will have done what is required of you in your work, so that you will not be accused of cheating or making a deal with the contractor later on.
It should be noted that if a person seeks to please Allah by angering people, Allah will be pleased with him and will make the people pleased with him.
So strive to please Allah, may He be exalted, and do not fear the blame of anyone for the sake of Allah.
“And whosoever fears Allaah and keeps his duty to Him, He will make a way for him to get out (from every difficulty).
3. And He will provide him from (sources) he never could imagine. And whosoever puts his trust in Allaah, then He will suffice him. Verily, Allaah will accomplish his purpose”
We ask Allah to help and guide you.
And Allah knows best.