But we still don't know what the hell Dark Matter is supposed to be, so that's a nice playground. For all we know at the moment, it could very well be giant amounts of cottage cheese.
Poul Anderson says in one of the Flandry novels that there are a huge number of rogue planets (planets not in a star system). That'd account for some of the missing matter.
As for making the replicators not work, they're what the Reeves'Stevens' called transtator tech - based on subspace effects, like the shields, warp drive, transporter, etc. I'd say that either:
A. You're not in another galaxy - you might think so
, but you're actually in another universe
. See Gene DeWeese's Final Nexus for an example of another universe's slightly different physics making problems for the heroes' ship. Or...
B. It's not a physics problem. Software or hardware malfunction somewhere. You will have to explain when they finally fix it why it took so long and was so hard to diagnose.
If you go with A, then the replicators will be joined by the warp engines, impulse engines, transporter, etc. in not working.