Not only is it common, but it's actually a useful thing to have your work be the mixture of two familiar things, because assuming that you want to sell your story eventually, that becomes a really good way to pitch your story: "It's Jane Austin with zombies," or "it's The Hunger Games in space" (Red Rising), etc. These make good pitches because they use instantly recognizable things, it's easy to understand, and if it's a good combination, then it will immediately spark ideas for the listener (ooh, I'd like to see how that would play out...).
Part of your question was about specifically combining two stories together, rather than a story with a theme or something like that. Part of the difficulty of answering that question is that it's pretty subjective to decide when to classify something as truly "being" a story vs just borrowing from it.
Example: you could describe The Matrix as Brave New World meets Alice in Wonderland. Ok. To what degree is The Matrix really specific to Brave New World as opposed to just the genre of dystopias in general? Well, the protagonist is intelligent and on a question to get outside the controlled world to a ragtag group of people who are living a more real lifestyle (The “Savage Reservation” in Bernard Marx’s case. For Neo, it’s the world of the Nebuchadnezzar). Also, Brave New World is a make-everyone-happy kind of place, as opposed to, say, 1984. So I could see an argument being made that The Matrix is more similar to Brave New World than to some other dystopias. But overall, if you put a gun to my head, I would say it’s more accurate to just say that The Matrix is a dystopia rather than that it's Brave New World specifically.
And what about Alice in Wonderland? The Matrix has a lot of overt references to Alice In Wonderland, and the plot starts off with the skeleton of it being similar: Mr. Anderson goes down a rabbit-hole (a portal that leads to a completely different-looking world that exists right alongside what he had previously thought of as the "real" world). But, most of the main events of Alice in Wonderland don't feature at all in the Matrix. Thematically they're both kind of trippy and all about redefining reality, waking up is a theme, etc, and there are lots of overt references...where do you draw the line?
So with that said, I would reframe your question a little. If you ask how often that a story is blatantly and unarguably two different stories combined, that's going to get messy really fast. But do stories reuse other stories and themes that have been explored before by other stories: YES, and in fact when you frame it that way, I think that 99% of stories probably fall under this umbrella.
If you have a story idea that combines to separate stories into one idea, that's not a bad thing. If anything it's a good sign because that is a tried-and-true way to make good new stories. It's actually when people try to be overly "original" (at the expense of everything else) that you get unreadable things. So yes, I think you're on a good path.