With all due respect, you're nuts if you're comparing two professional >$1500 lenses to a ~$100 lens. Even just comparing autofocus performance, they're not in the same class.
I'm really not bad-mouthing the 50mm/1.8. It's fantastic for the money. It's better than 1/15th as good as the L-lenses, but it's still not much of a comparison if price is ignored. When you start to be limited by its shortcomings (including sluggish autofocus) it's time to upgrade, probably to the 50mm/1.4 unless you're planning on the highest level of pro portrait work.
I am not comparing the 50L to any other Canon 50mm lenses. I know without a doubt the quality of an "L" lens (One reason why I don't bother buying a lower end Canon lens to begin with. Not because I can afford it but because I will bypass any upgrade therefore saving cost in the long run). As so many people have continually bashed the value of the "L" version in the recent review of the 50L, saying how overpriced it is and how good the more affordable 50mm 1.4 is in comparison, I was merely extending the benefit of the doubt to its sibling the 50mm 1.8.
As for the question I'd directed at the original poster, I was merely trying to help by first eliminating other possible factors before focusing on the limitation of the equipment. Nothing more than that.
This may have more to do with the way you shoot and focus or the way you set up the AF area selection modes with your 5DM3. How are you focusing and what AF selection mode are you using? I rarely have hunting issues with any of my lenses in lowlight situations, especially with the 24L II or 50L.
Honestly, with the wording you've used, the way it's interpreted for me is that you're assuming poor technique before thinking about the limitations of the lens. Instead of opening up with the question, you start with a statement like "This may have more to do
with the way you shoot and focus.." And then you said "I rarely have hunting issues with any of my lenses.., especially with the 24L II or 50L.".
That's like someone saying my Toyota Corolla can't reach speeds of xxx, and then you come in and say well it must be your bad driving because my Ferrari can do that fine.
Also note the OP stated that the focus hunting is only a problem with the 50 1.8, his 24-70 snaps on focus almost instantly, so clearly, not a problem of poor technique.