I remember a Tunisian friend who was fairly learned mentioned a few places (halachically, not geographically) where Sepharadim do not go by the SA, but can't remember the specifics.
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In Hilchot Chabbat (253,4), the SA says that you should not put hot water from a keli rishon into an other one. The minhag of the North African Jews is to do that (I heard that from a Tunisian Rav and we could find that in Shout Shemesh Oumaguen T1 s. 8,15,19 and 21 written by Rav Shalom Messas).
For the hadlakat nerot (263,5), the minhag of the North African Jews is to bless after the hadlaka like the Rama. (Cf Aley Hadass which compilates the Tunisian minhagim)
Regarding wearing a watch with teffilin on . The Shulchan Aruch 27:4 writes one shouldnt wear anything that makes a sepration between the teffilin. However,the Rama there notes that only os talking in a case of the batim not the arm or hand. The Sefardim seem to be maikel(Yacve Daas- Chacham Ovadia) while the Ashkenazim are machmir.
Many Sepharadim uphold the custom of Kapparot to this day despite Maran's objections. See my answer to this question for further information.
Whenever there is a machloket between the arizal and the SA we go after the arizal (see the peticha of ohr letzion)
-- Ovadia Yosef zt”l and many other poskim rule that a blind man can receive an aliyah, in contradiction to the Shulchan Aruch.
-- One does not recite a second blessing when putting a tallit back on after having removed it for as short time.
Discussed here as a side note to a different question on mezuzah:
"Although in general we follow all of the rulings of Maran Ha’Shulchan Aruch, Maran Ha’Chida writes that in instances such as these where many Poskim disagree with Maran, we must be concerned with the prohibition of reciting a blessing in vain even in opposition of Maran’s ruling. Thus, halachically speaking, as long as one had in mind originally to wear the Tallit again soon after removing it, one does not recite another blessing."
I definitely remember a few more of these including one with the statement "If Maran HaShulchan Aruch had only had this source in front of him, surely he would have ruled X."
Kedusha - the Shulchan Aruch (Orach Chaim 125) rules that only the parts that the Tzibbur recites is Kadosh Kadosh and Baruch Kvod... The Arizal said that the Tzibbur should recite all of kedusha with the Chazan. The Sephardic Minhag (although this is also followed by Ashkenzim, aside from Briskers, supposedly Yekkes, and interestingly the Yeshiva Beis Yisroel in Neve Yaakov Minhag , and those who follow Minhagei Hagr"a) is to follow the Arizal.