it can be a bent or worn pilot, the wrong sized pilot, or just poor machining practices by the person performing the work.
depending on the type of equipment used, operator finesse is more or less of a component of the final result.

for instance, if the equipment being used is of the live pilot type, then its pretty much mandatory to level the column to each individual guide before cutting the seat.
the seat cutter and pilot are positively attached to the column, and will cut square to it. if the column isnt exactly square to the guide, you'll get runout.
how much runout depends on how far off the column was in relation to the guide.

if its a "production" type shop using that type of equipment, and they level one guide and then cut all the seats referenced from that one leveling operation....you'll have one seat thats pretty good, and the others can be off a fair amount.

the ball driven seat cutters running on a fixed pilot are somewhat more forgiving to having the column being "dead nuts" square to the guide, since the cutter is riding on the pilot, which is fixed into the guide, and there is some room for misalignment in the ball drive, although its still best to square the column to each guide.

another possibility is the equipment being used isnt really the ideal set-up for machining seats(I.E; a seat cutting system being used with a milling machine isnt all that user friendly), and will require a more skilled operator to achieve consistantly good results.

some types of seat machining equipment is just easier to use than others.

the bottom line is, some shops seem like they are always in a hurry to get the work done.
unfortunately, some operations just require more time be devoted to them if you really want them done "right".

when you combine an unskilled operator(or an operator who just doesnt really care) with equipment thats unforgiving, you're not going to get positive results.