All plasma cut edges will have some bevel, typically around 3 to 5 degrees. This is especially true for holes. When i am cutting bolt holes, I always draw the hole larger (same as what @oneupperformance described). Over time you will get a feel for how much larger you need to make the holes in order to have the bolts go in.
Now if I am doing a part that has critical hole size requirements, I will cut the holes on the plasma significantly smaller than the final size. The reason is because the plasma cutting process creates a very hard nitrided layer that is about .015" thick. If you try to shave off .010-.020 with a reamer or a drill, you are likely to trash it very quickly. Now, if you plasma cut the hole .100" or so undersized, the cutting edges of your drill will be able to get under the hardened surface.
One other tip, always drill from the back side of the part as it will further prolong drill life.