Putting the filter in back introduces focus shift, so you have to be sure to focus with the filter in place. Dirt or scratches will also have a greater effect behind the lens than in front.
On the other hand, you don't have to worry about shading the filter, if you put it behind the lens.
In an ideal world, I'd always use filters with a compendium bellows in front of the lens, but in the real world, I've got too many weird old lenses with odd filter sizes for this to be practical. I also have a few ultrawides that just can't take a filter in front without vignetting, because even a step-up ring for a larger filter will vignette. So for those lenses, I have 3x3" filter holders epoxied to the back of the lensboard, and I put the filter behind the lens.