Did you hear Paul Wylie say that there are no mandatory deductions in the SP anymore?
He's not quite correct about that.
The "deduction" function has been divided up between the technical panel, which assigns deductions for falls, incorrect length of program, illegal elements, etc., and the judges' (negative) grades of execution, which are referred to as "reductions."
Some mistakes are penalized exactly the same in the short program as in the long, and some are penalized more severely in the short program because the short program requirements are more specific.
For example:
I think Wylie made that comment in relation to Yuna Kim's triple flip-single toe combination? For a mistake like that, in the long program, there need be no reduction in the GOE -- 0, +1, or even +2 would be possible if both jumps were well performed. With a hand down on the first jump, -1 would be the most likely GOE.
In the short program, the combination is required to include either a triple jump and a double jump or two triple jumps. Triple and single doesn't meet the requirements. The GOE is required to be -3. (In fact one judge gave Kim -2 for that element at the GPF, but that was incorrect and it was thrown out anyway.)
In addition, as Wylie noted, the reduced GOE is taken off the base mark for the jump rotations actually performed, not from a base of the triple-triple we know she had planned or of the triple-double that would have been the default assumption in that kind of situation under the old system where base marks were set for whole programs instead of individual elements.
For a clean triple-triple, Kim got 11.5 points (all +2 GOEs) in the long program at the GPF. A triple-double with no pluses or minuses would be 6.8. Triple flip with hand down-single toe in a long program with good quality it could be over 6 points; with the hand down it would probably be 4.9. In the short program, with the hand down or even with good quality, the triple flip-single toe is worth only 2.9. So at least 2 of those points, or possibly more than 3 points, could be considered "deductions" specific to the short program.
Similarly with Kostner's single axel. In the long program that would be a perfectly legal jumping pass and could get full credit, with base or positive GOE depending on the quality of the axel, with the base mark for the single axel (0.8). In the short program, double axel is required, so the single starts with the base mark for a single axel and then gets -3 GOE reduction. A double axel base mark would be 3.5; a good single axel in a long program could be 1-point something; Kostner ended up earning a whopping 0.3 points for that element.
In both those examples, the loss of base mark for the single instead of the double or triple jump is a bigger penalty than the reduction in the GOE, but that reduction required for doing the "wrong" jump in the SP is not required in the LP.
Also, the short program spiral sequence requires three spiral positions held for at least 3 seconds and requires a change of foot. Long program requires only two positions and does not require the change of foot. (Almost all skaters who do spiral sequences do include the third position and change of foot in the long program because it's necessary to do so to have a chance of earning level 4, but the penalty for not doing so is much greater in the SP.)
For example, suppose the skater chooses to do a left forward outside layover spiral, change edge to left forward inside Biellmann spiral, and then a couple of strokes to right back outside Charlotte. That would be level 4 if performed correctly, and the GOE could be very positive if the edges and positions are good.
Now suppose that the skater is behind the music and ends up holding the final (backward, right foot) position for only 1.5 seconds so she can hit her next element on the correct beat as choreographed.
In a short program, that would mean that there were not three positions held for 3seconds and there was no position on the right foot held for 3 seconds. So regardless of how well she did the first two positions, the technical panel is going to call the sequence as level 1 and the judges are probably going to reduce the GOE by -2 from what it would have been otherwise.
In the long program, the sequence would still qualify for at least level 3 and could still get positive GOE.