Much depends on where the car spent most of its life. My 560SL, only 4 years older than yours, started out in Florida and then languished in Mass. until I brought it to Canada a little over a year ago. I suspect the Florida salt air contributed most to the rust on the steel lines on the filter assembly. Interestingly, only one was in good condition, somehow avoiding the plating deterioration which will rust the line in no time, once it starts.
If you didn't examine the condition of the line(s) before they started the work, perhaps they still have the old one(s) to show you. IMO, this sounds like a legitimate charge, part cost being dependent on which line broke. On my SL, I know at least one was well over $100.00, aftermarket IIRC, so dealer cost would be more.
I had to remove the entire pump/filter/accumulator assembly, perform a major parts replacement and overhaul.... but I digress, as that isn't relevent to your situation. Suffice it to say that the first 1/8" turn of the wrench at the filter connection was enough to rupture the steel line.
Regarding the hose pieces, again, rubber goes south with age, and we're looking at nearly 20 years on your car, at a rubber hose that spent it's entire life about 6" from the ground. If they pinched one of them to do the work, standard practise, that would easily do it in. I avoided that by doing it the 'messy way', nearly empty tank, drain into bucket method, lots of fuel up the arm and on the floor, goggles over eyes...you get the picture, why they'd avoid doing this.

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1986 560SL
2002 Toyota Camry
1993 Lexus