Talk to your builder first; if they do not change to comply with your contact, then you need to consult with your lawyer.
When I bought my house, we also found several builder's mistakes, such as reduced window size (early building stage), missing one sink on a double sink counter in the bathroom (late building stage) and a missing a light in bedroom (after closing but before one year warranty expired). The builder (although it's not Minto) fixed them without involving the lawyer.
In your case, I think it's easy to have the builder install the missing windows but specified by your plan and contract - if you insist and want them. But it might be hard to have them remove your neibough's - at least it would be a lengthy argument.
