Yes. I experience this quite often. Unfortunately no one has offered up a solution. I was told it all depends on the size of your database and the complexity of your smart list.
I often have trouble with this as well. I've contacted Marketo support in the past, and I was told that I would have more luck pulling smart lists (and reports) in off-peak times. I find that I have more luck at the end of the day instead of the morning. To get around this in the past, I have created smart campaigns to push people into static lists. Once I had my static list, it was much easier for me to export the data.
I've run into this problem as well. I usually see if there's a different way I can pull my Smart List if there are a lot of filters, like using 2 smart lists to pull in separate parts of the list, and a main Smart List to pull the other two together.
Hey Justin Berger - here's a trick I use for my monthly reporting that utilizes some crazy, crazy smart list logic: I create a static list, then a Smart Campaign. The Smart List in the Smart Campaign contains my Smart List logic, and then the Smart Campaign has a single flow step - add to list. I can then schedule the lists to run at night so I can see the leads that qualify when I come in.