A lot of the problem with that comes from the classification of races though, the CQ ranking has separate points scales for GT1 (Tour), GT2 (Giro/Vuelta), WT, .HC, .1 and .2 races, with the same applying to one day races with the Worlds and Monuments counting for more. One of the biggest problems is simply the classification of races, i.e. that all WT races outside of the GTs are ranked the same, and that a lot of pretty meaningless, worthless pre-season races are .HC mean that you can get a truckload of points in those.
The other issue is balance of points one-day vs. stage races, as evidenced by the year Murilo Fischer was in the top 10 CQ points for the year on a ProConti team because he went ballistic in a bunch of late season 1.HC and 1.1 sprint races in Italy. Even outside of that, stage races that favour flat racers like Kristoff can often provide more points because they'll be up scoring stage points every stage whereas in a mountainous stage race often time gaps are bigger and so you don't have the top riders contesting the stage win every single day. Also, the 110 points for a 2.1 race pay no mind to whether it's two days (the shortest ones) or eleven (the Volta a Portugal) - so somebody who is doing a bunch of short flat stage races and one day races preparing for the Classics will have a lot more points available than somebody doing a race like the Giro del Trentino or the Vuelta a Burgos to prepare for the Giro or Vuelta.
And really, Hayman won Paris-Roubaix but didn't do much else all year so it's no surprise he's not THAT high on the list. Zaugg didn't make the top 10 in 2011 either - ranking 105th with 489 points, 275 of which were for Lombardia. Hayman scored 377, of which 280 were for Paris-Roubaix. And Zaugg had a much better year in 2011 than Hayman did this year. Until Roubaix Hayman hadn't made the top 75 of any race in 2016; the only other top 20s he had all season were the Tour de Luxembourg prologue, one stage of the Tour and the Japan Cup. None of those were top 10s. His best placements other than Roubaix in one-day races were 14th at the Japan Cup, 21st at the Worlds, and a marvellous 28th in the Cadel Evans Great Ocean Road Race. The next was 76th in the GP Miguel Indurain. His highest stage race position was 31st in the Tour de Luxembourg. Zaugg had 4 more top 10s outside of Lombardia, the nationals, one stage of the Vuelta, and two Italian 1.HC and 1.1 races leading into Lombardia, plus 11th in another.
Really, Hayman didn't have a good year. He had one great race day, and it was a memorable and exciting one, but Kristoff has been there or thereabouts all season. The problem is that because of the reasons I point out above, Kristoff picks up a lot of points for races like the Driedaagse van de Panne - because of winning the first stage, and being 3rd in two more, he scores 45 points. For defending the leader's jersey for three stages he gets 24, and for being 2nd overall because it's a flat stage race and winning the only tricky stage plus bonus seconds put him in a strong GC position he got 120 - total 189, and then he was 4th in the Ronde van Vlaanderen which yielded 125.
Perhaps the biggest flaw CQ has is that it doesn't differentiate the more prestigious races at a ranking level from the lesser ones, so the likes of Abu Dhabi give as many points as Dunkerque and Burgos, for example, and that victory and/or the podium is not sufficiently separated from relatively anonymous placements. But what CQ CAN do is neutralize any issues inherent in the WT race selection. This is less a problem with the men but among the women it's been very clear that the bias towards flat and moderately hilly races in the WT races (often promoting borderline crits in the aim of taking the racing to fans rather than promoting established and historic races, which I have had many gripes about, especially as the WT looks to be trying to screw over the Thüringen Rundfahrt and the Emakumeen Bira, two of the toughest stage races around, to make room for its expansion races and the 66km ASO BS festival) has had a direct effect on the WT scores compared to CQ which balances out this with the scores for non-WT races, and the Boels domination is far less on CQ than in the WT scores as more climbing-adept riders are much better represented in the CQ tallies to give a better balance between rider types.