Under the contract, only the Project Manager can instruct a change to the Work Information or Scope (under NEC4), unless an individual is delegated authority to act on the PM's behalf. So contractually, unless this delegation happened the Contractor should have ignored the engineer or ideally, early warned the PM saying 'do you want me to do this and if 'Yes' you either need to delegate powers to the engineer or instruct yourself ... and going forward, can you sort out your project organisation so this does not happen again!'.
Assuming the engineer, did not have the authority, if you wanted to be hyper contractual, you could dismiss this additional work as never being instructed. However, you do have to bear in mind effect on relationships and whether this work was actually needed i.e. would the PM have given the instruction in any case. Otherwise, the Contractor could dismantle the additional work to salvage some cost.
Assuming the engineer, did not have the authority, if you wanted to be hyper contractual, you could dismiss this additional work as never being instructed. However, you do have to bear in mind effect on relationships and whether this work was actually needed i.e. would the PM have given the instruction in any case. Otherwise, the Contractor could dismantle the additional work to salvage some cost.