The difference in this case is that a practical P (complexity class) algorithm for factoring is something that theoretical cryptographers worry about. It's not some fantastic or unexplained or misunderstood item, like most macguffins are.
In a somewhat overly literal sense, it is fantastic, simply because it isn't real.
The Hollywood cliche is more where the singular genius that only built the one device ended up dead, along with any notes and research hinting at how it might work.
The other big fallacy was the notion that you could magically gain access to any system as long as you could crack their encryption, along with the computer systems magically decoding to show graphics IIRC.
None of the systems required you to be running their custom client software, and all were accessible through public networks or dialup.
Didn't break the movie for me, but it's definitely something I notice.
I don't know it was a Hollywood cliche or just a general fiction trope, there's been boxes of power going back to early story days, things are hard to get away from in story telling.
