This really does happen all the time, it doesn't matter who you're talking to. Its really hard to avoid. When you're the one talking, you have a mental picture in your head. You're just trying to convert that to words so other people will see it too. But the people you're talking to don't have the same mental picture, so "it" could mean something completely different to them.
You're really trying to shape their mental picture to match yours while continuously updating yours to reflect theirs, so you have to be very specific until you can settle on some common terminology to represent that picture.
I like to use Personification to make this go smoother.
the attribution of a personal nature or character to inanimate objects or abstract notions, esp. as a rhetorical figure
I like to take this one step further and make the people I'm talking to represent the various components of the system. Person A is the database, person B is the website, person C is the application, and I'm the Document Management system. I've found that this works really well. Now I can say "You wont store versions, but I will" instead of "The website wont store versions, but the Document Management system in the application will."