Have you got any pictures of the bumper? It might be worth posting them here for a second-opinion. I once had a Vauxhall dealer try to fob me off with some really shoddy work. The car went back to them several times before they actually sorted it.
Also, another bodyshop might be prepared to give you a free second-opinion on the quality of the work. I took my Astra to another Vauxhall dealer, who agreed that the repair had been carried out very shoddily, and pointed out several other things that I hadn't even noticed. Unfortunately, he didn't want to go on record with his statement, and to be honest, I can't say I blame him. But he gave me some more ammunition to go back with
If this was just rear-end damage, then they're unlikely to have disturbed the gear shift linkage. On the other hand, if they've 'jigged' the car to straighten things out, then I suppose anything is possible. Ask them if the car has been on a jig - if it has, then insist that this has probably moved the engine and gearbox in relation to the gear selector and knocked things out of alignment. It should be a simple enough adjustment to put it right.
If there was front end damage and they tell you that the car hasn't been on a jig, then get the geometry of all four wheels checked out by an independent. The car may need jigging after all.