Hardware technical difficulties experienced at the end of the game (spoilers)

[Abion47]

Here's the full conversation where they discuss the subject:

S: "Do we need to turn it off? Can't we just keep him alive until we've got the cipher?"

C: "The longer he's exposed to the computer model the more he'll get hung up on it."

S: "What's so wrong with letting him settle in a little?"

C: "It would drive him insane. So let's keep the sessions short and the suffering to a minimum."

...

S: "Does anything carry over? I mean, could he remember this hell we're putting him through?"

C: "The simulation never affects the scan pattern. Each time is a fresh start."

S: "That's a little comforting, I suppose."

So strictly speaking, regarding Brandon at least, there wasn't any danger of him overloading the systems, and it was more a matter of ethically terminating the simulation before the subject suffers from unnecessary mental stress. However, I feel like the situation with Catherine and the Omnitool is under different circumstances. For one, it's not a simulation in the same way that Brandon was. Brandon was placed within a virtual world, whereas Catherine exists in the real world (albeit in a computer chip and only perceives time passing while she is plugged into something).

Also, keep in mind just what that chip is. It's a cortex chip, a piece of modular electronics designed to house an AI that will operate a piece of equipment with relative autonomy. It wasn't designed to run an AI as complex as a human brain scan, though, so the power and processing capabilities would have already been stretched to their limits. It was also caked in structure gel, so it's safe to assume that it has been compromised in some way. Finally, if you're paying attention to the display on the Omnitool or on the image of Catherine whenever you plug her in somewhere, you can see that the Omnitool is degrading over time.

Then consider the ARK simulation in the downstairs lab at Theta. With each new module that the simulation had to run, it increased the storage and processing requirements of the simulation itself. For Catherine, it would make sense that running a "process" like complex and extreme emotions would be another "module" that the chip would have to run, and given the state of the Omnitool, it's a safe bet that her losing it would finally drive it past the breaking point.

Now a fair amount of this is based on assumption and conjecture, it's true. But I choose to believe that this is the reason for Catherine breaking if for no other reason than the alternative is not satisfying. If it wasn't this that caused the Omnitool to break, then we would have to accept that whatever the cause was, it was a massive coincidence that the Omnitool happened to break just as Catherine was reaching the peak of her anger.