This is not a common problem but happens often enough that it’s worth understanding.
The pattern swatch is often vector based. If it is sufficiently complex and several clipping paths are used they can time out at prepress. There are obviously work arounds… The perfect example is when one fills a bunch of tiny areas (paths) with the swatch.
I believe what happens is that the code was written poorly in that what seems to be happening is the computations are out of order. I think (and I could be completely wrong) that the entire swatch is computed first as an object, then it is cut by the path - cut by any other path… It should be the other way around so that only the path is filed instead of the entire 2" square (plus the extra computations). This isn’t a problem with a color or a gradient since there is very little information to be calculated.
When one has hundreds of tiny paths, all filled with a 2" x 2" pattern, the time-out occurs.
Like I said, the best way I’ve found to fix this is to isolate and rasterize the layers with the swatch but that can be time consuming. If anyone knows any other tricks, please pass them on.