Hello and welcome!
Short answer:
Your company most likely is doing things right. Since the construction of a new facility is a big project, it is very common for companies to issue a specific Validation Master Plan (VMP) for the project since most elements of the VMP are impacted. So, the change control that was issued for the construction of the facility, lead to the issuance or change of a VMP, which as consecutively lead to the issue of all validation and qualification activities. This way, even though the validation protocols are issued as part of the updated VMP, the modification of the VMP was derived from the change control.
Unless there were no change control issued to begin with which would be big problem.
Full answer:
By the way you described the situation, it leads to thinking that the company did not issue a change control for the building of a new facility, which is serious deviation. The applicability of a change control should not be limited for changes in already constructed facilities, but should apply as well to put new facilities in operation and to put them out of commission. Pharmaceutical Quality system (PQS), which obviously includes the Change Management System, applies for all GMP related activities, including the construction of a new facility.
That point aside, all Validation activities must be derived from the PQS, the Validation Master Plan (VMP) is part of the PQS, just like the change control, and while most of Validation activities are expected to be derived from a Change Control, not all of them are. Take, for example, periodic HVAC verifications/requalifications. These periodic verifications are set by the VMP to verify if the HVAC systems remains in compliance with qualification criteria, based only on a period of time as requested by the VMP and not by a change control.
However, in this case, the construction of a new facility, as per GMP, must be managed by a Change Control, where all risks to quality of the product are being diligently evaluated and mitigated. As a result of using this risk based approach, the need to Validate and Qualify should come as part of the action plan of the change.
Since the construction of a new facility is a big endeavor, it is typically managed as a project, where a big change control governs the project, and several smaller change controls are issued to better manage different aspects of the project. It is also very common to issue a specific Validation Master Plan (VMP) for a huge project like this, since most of the elements are impacted. This way it is much easier to manage validation activities for a big project like the construction of a new facility.
As for guidelines, look for ICH Q10 which talkes about the Pharmaceuticla Quality System. FDA and most other regulatory agancies are based on this guideline.
Sorry for the long answer, but I hope that this was useful.