Pellets, as manufactured, are _very_ smooth. This is a decent overview I just found from Google: http://www.world-nuclear.org/info/Nuclear-Fuel-Cycle/Conversion-Enrichment-and-Fabrication/Fuel-Fabrication/#.UVmkjas5yZc
They start life as powder and then are packed in a way that makes them smooth.
However, just as in any kind of manufacturing: defects happen. A working reactor will have over a million pellets in it. Somewhere in there one is going to be misshapen.
Some of what we can do is run a ton of statistically guided calculations to understand what kind of safety and design margins need to be in place to keep problems from occurring. We can also look at modifying the design of the pellets to insure safer operation. Both of these things are very difficult (and costly) to do experimentally.
My lab (INL) does a lot of experimental fuel work... but we use these detailed simulations to guide the experiments so we can use our money more wisely. It literally takes years to develop a new fuel form, manufacture it, cook it in an experimental reactor, let it cool down, slice it open and see what happened. Using these detailed simulations we can do a lot of that "virtually" to help them decide on experimental parameters so that at the end of that whole sequence they have a bunch of _very_ good experimental results instead of half of them just being failures...
Also, we do actually have a bunch of detailed experimental results to compare our simulations to. Even with this fidelity of modeling we are still not able to perfectly capture what happens in all of those experiments. Even more detailed models (like the multiscale one in the video) need to be developed to be able to truly predict all the complex phenomena that goes on in nuclear fuel.
There is still a LOT more work to do...