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If you don't get the spec right in the first place - all the above will happen, and the MoD will blame the contractor.
Long time since MoD were allowed to write specs; or indeed consciously employed anyone trained to. What happens is you get a fanny URD from London and quietly, without telling anyone, draw up a "clarification paper" (spec) and slip it in the envelope to bidders. And just hope it's a fatter envelope than that tabled during the "political impact" lobbying.
In the mid-90s I spent 2 years on a competition for a new Mark of aircraft. Only one of 4 bidders was remotely compliant. One withdrew because it was too difficult. On the verge of awarding the contract to the runaway winner, a political overrule came down - it was to be awarded to a company who hadn't bid, but who happened to be (conveniently) relocating to a constituency whose MP had lobbied best. They were then bought out by the company who'd withdrawn. Each spent millions not realising they were in an unfair competition. Bidding for that job meant they couldn't bid for others. (Who has multiple bid teams for whole aircraft?) They recouped the cost by simply increasing the price next time. Good job we had Boscombe and Westland to step in and do most of the job. I've lost count of how many "RMPA/N2000/MRA4" and "Chinook HC3" gold standard cock ups we'd have had without those two.