Generally bearings are counterbored into the liners....so let's say your using .050" liners..... not enough material for the necessary counterbores, so you need to increase liner thickness for the bearings. OR If the blade thickness is enough, you could put counterbores in the blade..... or even 1/2 in the liners, and 1/2 in the blade. Just a whole host of "little" things that can cause grief.
Sometimes using bearings on a knife that was designed with washers in mind, will force you to change the location of things such as the stop pin, where/how the lock is cut and/or engages, etc. There are certain things with folders that you can change, without affecting anything, but when you start changing "internals", one thing often affects another....and you end up having to do a bunch of "tweaking"....its mostly "small" changes, but it can literally eat up days of time. When I see this sort of thing happening, I've found that it's much more efficient to just "tweak" the entire design, (redesign) fixing all "issues", and then start the knife again.
On the other side of the coin, IF you initially design a folder in such a way that it can be built with EITHER bearing or washers..... you're a step ahead of the game. What I've discovered over time is that if I design a new folder with bearings in mind, its a very simple thing to retrofit the design with washers.....but it general doesn't work well, the other way around.
With that in mind for a number of years now, whenever I create a new folder design, its always with bearings in mind..... just makes my life far easier.
I'm sure everybody has there own unique way(s), but that just how I see, and how I tackle the problem.