There's a lot of weird ships in Danganronpa...but in general, these are the main ships I have problems with:

1: Despaircest (Junko x Mukuro)
One, incest.
Two, I'm pretty sure any ship with Junko would have abuse rolled into it. I'd prefer to see Mukuro shipped with someone who'll help her-like Makoto or Sayaka.

2: Junko x Mikan
Mikan's been through hell already. Why do people ship her with someone that'll give her more???? No just no.

3: Korekiyo x His Sister
Again, incest. And possible abuse.

I hate it if it is abusive and involves incest.

Honorable mention:

Toko x Byakuya

First of all: toko=stalker
Second of all= that can't exactly be the healthiest ship for either of them.