These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: The Ark of Truth
Continuity Lock-Out: This was put together to be the finale, and resolve as much of the last two seasons as the writers could. So naturally this wasn't going to make sense to those who hadn't watched the last two seasons, which is why DVD of this film came with a recap of those seasons, to at least try to get people up to speed.
Mitchell:(paraphrased) Don't worry, guys, I killed the escaped Replicator, which had been hanging around unsupervised on our spaceship for a while! We're totally safe now! The only possible way we could be in trouble is if Replicators were somehow capable of making more of themselves! But that would be ridiculous!"
They all knew that the Replicator could make more of themselves, they were just hoping they could kill it before it did.
It was a reasonable assumption, since he had only seen/heard the one Replicator and only a couple minutes had gone by.
Nobody thought to bring a P90 or a sidearm when dealing with the original Replicator? Sure, you might not want to pop a hole in the ship but it's a hell of a lot better than the alternative.
IOA agent James Marrick and by extension, the IOA as a whole. The sheer stupidity that went into the idea that they not only knew how to deal with the situation better than the people who'd been doing this sort of thing for years, and thinking that they could use the Replicators without suffering any ill consequences goes far beyond Too Dumb to Live.