It is not the tech that makes the plot holes, but the author's understanding of the tech he writes about
When introducing a technology, I like to start by trying to invent the science behind it before I try writing it into any scenes, and then asking myself how many different technologies I can build off of what that one thing brings to the table. When you start off, don't dismiss any application of the technology you come up with no matter how broken it is. Infinite power source, something that can destroy the whole universe, does not matter. Write them all down, and don't start writing this tech into your stories until you've had a few days to mull it over. Some good questions to ask are:
- How can I make a weapon out of this?
- How can I make an engine out of this?
- How can I make this into a fuel source?
- How can I communicate with this?
- How can I make existing industries obsolete with this?
- How will this be used by the sex industry?
- How can I make a product for mass consumption with this?
- How can I make a premium product for exclusive consumption?
- What is the best thing I can use this tech for to make society better for it?
- What is the worst things I can use this tech for to make society worse for it?
- How can I combine this tech with other sciences I'm adding to my story?
- And finally, how can I combine the above answers to make even better inventions?
Once you ask enough of these questions, you will often find you've invalidated some aspects of the world you want to make; so, once you get here you need to introduce rules into your technology that limit it enough to tie up the exploits. Then ask all of your questions again to see if you can still exploit the system, and if the system still gives you all the abilities you need.
Let's take the replicator example. Those things are crazy broken if you don't put some limitations on them. Open ended replicators basically say you can make any weapon or material out of nothing which entirely invalidates all industries, currency, and hardship and makes pretty much everything free. This is a terrible invention for creating plot points that can't always be solved by just replicating things, but with a few small limits, they are not so bad.
Let's say your replicators can assemble molecules, but it still needs a reserve of all the needed base elements. This means you'd still need to mine for all the iron, aluminum, titanium, carbon, etc that a replicator uses, but that the replicator just puts it together. This way, if you want to replicate a hand phaser in one scene, then latter you need to go to a port to get a new phase coil for your ship's main guns, you can simply say you don't have enough tungsten left in the replicators to fix the main guns.
But, maybe making phase pistols should also be off limits, and you just want replicators to be something people use for thier morning coffee, you can then also add limits about some elements perhaps being too unstable or heavy for certain replicators. For example, you may have class 1-7 replicators which correspond to how many rows down the periodic table your replicator can handle. Sure, with enough time and knowledge I could just make a class-7 one, but class-7s are enormous, and require a thousand kilos of antimatter to make a cup of coffee; so, people always install the weakest replicators they need where they need them. This way you make it so that someone can't just walk up to a class-2 food replicator and churn out a gun, but perhaps a particularly clever assassin might use one to make a polymer based gun entirely out of light elements.
Basically you just keep adding more and more rules until the exploits left sound like they are cool solutions to hard problems and less like shortcuts around having to work for your goals.
Next, you need to ask how replicators work alongside other technologies in my universe. For example, if I also have teleporters that can turn people into energy and transport them over long distances, then I need to limit them to only being able to transport elements that a same level replicator could handle. Otherwise, why wouldn't people just use transporters to replicate things? This means that I may not be able to beam down to a planet surface with my scientific gear, but a person and polymer clothing would be fine. Transporter tech should also imply that replication at a distance is okay too; so, then I need to look for all sorts of applications for ranged replication like weapons that can disintegrate a person into thier base elements, commercial replicators that allow you to order something more complex online than your home replicators can handle and have it replicated for you right in your own home, mining beams that disintegrate base elements from ore transporting them up to orbital mining platforms, and replicating medicines and poisons directly into a person's bloodstream. These are all things that as an author I should come to terms with EARLY in the world building process, before I commit to a single scene of plot, because once you publish plot, it's too late to handwave away the unintended consequences.
Lastly, engrain this tech as deep into your culture as is appropriate for how long they have been around. If replicators are a new tech, they might be highly controlled by governments and militaries. If replicators have been around for over 100 years, they should be pretty much everywhere doing everything. Your toilet is just a replicator that decomposes your waste elements and stores it for your next meal. Your chess board has a built in replicator that materializes and decomposes your chess pieces when ever you want to play. Your closet is a replicator you step through that dresses you for the day. So on and so forth.
You will find that if you know and understand the applications of your sci-fi tech going into it, then even if you don't fully explain the tech every time you use it, that by the time you get to a scene where explaining something about it is important, that everything you've done up until this should already be consistent with the explanation; so, in Chapter 2 when your Chief Engineer says "I can't get fix that without a class-6 replicator" it might just sound like techo-filler to your audience, but then later in Chapter 7 when your Chief Engineer is explaining to your ship's cook how replicators work in detail, not only is chapter 7 consistent with chapter 2, but the scenes then add value to each other, because your reader might then get that ah-ha moment when he realizes what the big deal was about not having a class-6 replicator before.
As a Final Note: If you find you've left yourself vulnerable to an unintended consequence. Don't be afraid to put it into your story. If you've made disintegrator beams a possible thing in your setting, then it is better to have disintegrator beams than it is to try to avoid them leaving readers wondering why no one in your universe is smart enough to just come up with one.
