I would recommend figuring out which it is before getting excited. If the bolts fell out from vibration, then count your lucky stars, and use a paper clip or other device to determine how long the replacements need to be. I believe it's either a 6mm or 8mm thread, coarse pitch (M8 x 1.25 IIRC, not sure on the 6mm)
If, on the other hand, the bolts were broken off, curse and swear for about 5 minutes as you get to remove the air intake plenum to either drill out the bolts or replace the plenum. It's really not that hard, but it does take some time, especially if you haven't done it before. I would then start researching how to remove broken bolts. I've used both hydrochloric acid (swimming pool acid, many safety precautions to be worried about) and electrolysis to remove rust before, and have heard of folks using it to remove the rust from around these areas to help in freeing it up enough to be able to remove it without damaging the threads in the aluminum plenum. This of course is after the penetrating lube/easy out extractor doesn't work. Also, these methods are time consuming (on the order of days), so you have to compare that against the roughly $300?? to replace the intake plenum. Perhaps one could be had on ebay for less?
How many miles on the van? Depending on mileage/maintenance history, if you end up removing intake plenum, probably a good time to do new plugs/wires and valve cover gaskets (f you have any oil leaks in that area), as the same components must be removed to get at them. Also check rear heater lines at this time for rust
and decide if that will be replaced at the same time.
I'm not one to recommend just wildly replacing parts, just suggesting you evaluate if the items considered "routine maintenance" are getting anywhere close to needing service and attempt to kill several birds with one stone.
If you're just looking for someone to blame, then you need to know whether or not the bolts were broken before they replaced the fuel rail. I'm not certain, but I wouldn't say that it's impossible to replace the fuel rail without removing the plenum, so they may be telling the truth when they say they didn't mess with it when replacing the fuel rail.
2003 Honda Odyssey EXL (3.5L)
1997 Town & Country LXi (3.8L)
1992 Honda Accord LX (2.2L)
1990 Chevy K2500 (5.7L TBI)