
This one is shounen-ai but it's really good, it's the only one I can think of involving 'real' bullying: http://www.mangago.zone/read-manga/never_understand/?av=2
Summary: side/second couple - seme and uke were once friends, but they drifted apart due to [reasons], so the seme and his new group of friends bullies the uke in various ways. The main couple has a tease kind of thing going on but they're both going forth and back at each other.

http://www.mangago.zone/read-manga/g_senjou_no_neko/
There are two semes. The first one is kind. The second one is the bully.

Sorry not much of these involves actual bullying. But seme all hates/dislike the uke.
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My starry sky/cosmic boy
http://www.mangago.zone/read-manga/cosmic_boy/
(Actual bullying. Great story line. Shounen ai)
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If you hate me this much:
http://www.mangago.zone/read-manga/if_you_hate_me_that_much/
(Seme despises uke and sexually harasses him for revenge)
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Sick:
http://www.mangago.zone/read-manga/sick/
(There is slight bullying...umm..elementary level tho like tripping him or giving him hard time...)
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G senjou no neko:
http://www.mangago.zone/read-manga/g_senjou_no_neko/
(There are two semes. The first is kind seme. The second is a bully and sexually harrassing guy)
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Mujihina otoko:(part 1) http://www.mangago.zone/read-manga/mujihi_na_otoko/
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Mujihi na anata: (part 2)
http://www.mangago.zone/read-manga/mujihi_na_anata/
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Mujihi na karada: (part 3)
http://www.mangago.zone/read-manga/mujihi_na_karada/
(3 part story from the warui series. The seme HATES the uke a whole lot. No actual bullying involved but Seme despises the Uke with all his heart lol)
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Remnant kemonohito universe:
http://www.mangago.zone/read-manga/remnant_kemonohito_omegaverse/
(No actual bullying. Seme always fighting with uke. Much angst and hate and drama.)
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Misekake oresama kun:
http://www.mangago.zone/read-manga/misekake_oresama_kun/
(Not completed yet. No actuall bullying. Seme is annoyed by uke and treats him only as sex friend. Uke is misunderstood and totally in love with seme.)
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Free kisses:
http://www.mangago.zone/read-manga/free_kisses/
(No bullying. Seme hates uke's attitude. Always fighting the uke)
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http://www.mangago.zone/read-manga/gakuen_tengoku_sore_wa_koi_desu_koizumi_kun/
(This one, the uke does the bullying. And seme have strong feelings of hate for Uke, everyone thinks he bullies the uke but in reality it's the uke who bullies him)
Any yaois were the seme actually bully’s the uke of dislikes him strongly but then he starts having feelings for him. Not like teasing, like actual bullying or dislike.