In many cases, when you have a writer and producer and director involved with a film based on a historical work, it's because there's a passion for the work. That doesn't happen every time, but quite often that's what inspires the movie. I think this would mean they do understand they are two stories and enjoy the Alice books.
But then, from a production standpoint, you have a number of considerations that come into play once you're going to spend millions of dollars making a movie that you are counting on to not only return your investment, but to make a nice profit:
- They know they'll be making one movie, but can never count on the green light for the sequel. When you have a chance for profit, you don't hold back good material "in case" there's a chance for a sequel. Make the movie, make the profit, then worry about the material for the sequel.
- Both Alice in Wonderland and Alice Through the Looking Glass are highly episodic, so even though there's an overall plot, it is easy to pull episodes from each book and tie them together in one plot.
- The creative people behind the movie have their favorite elements of the Alice books and will want to include them, even if they stretch over two books.
- The viewing public is composed of people who, for the most part, will never read the books, but have expectations of an Alice movie. Everyone knows that Alice meets the Red Queen and White Queen and the Tweedles, the trip through the rabbit hole, the "Eat Me" and "Drink Me" notes for the cupcake and potion that make her big and small, as well as other elements from both books.
- This viewing public, for the most part, would be disappointed if their expectations are not met, so leaving out key elements of the Alice mythos, even if they're from two different books, would disappoint a lot of the public whom the producers need to buy tickets in order to make a profit.
From the production point of view (which is where the money to fund the production comes from, so it's the one in control), There's no reason to split the books and every reason to put in as many of the popular characters and situations into one big movie in the hopes of a blockbuster profit as opposed to withholding good material in the hope there will be a sequel.
Also, many fans and aficionados of Alice know the story and are often interested in the different interpretations and what each production brings to the mythos that is new. (And, yes, there are traditionalists that want to see perfect interpretations of both books.)
Additional Material, Not Directly on Topic for the Answer:
Back in the 1980s, there was a miniseries, produced by Irwin Allen (sorry, I know that name is close to a swear word in some SF&F circles) that aired over two nights, each episode being (I think) 2 hours. It included many talented guest stars and musical numbers, such as Ringo Star, Sammy Davis, Jr., and Steve Lawrence and Edie Gourmet. The first episode was Alice in Wonderland and was, if I remember, quite a faithful adaption of this book. When she returns home at the end, there is some kind of cliffhanger, like everyone is gone or there's something different, and this leads to the 2nd episode being an adaption of Alice Through the Looking Glass. As I remember, while this had most of the key characters and elements, it wasn't as true to the original as the first episode was. I know this is on DVD because I have it around somewhere and have been waiting for time to watch it (if I can find it again).
I'll add that, personally, I'd like to see a big budget production where the poems are done as musical numbers and both stories are filmed at the same time and released, say, six months apart that remains rather close to the structure of the two books, but I doubt we'll see that.