Counterpart type contradictions:

Branched Evolutions:

Vileplume : Grass/Poison
Bellossom: Grass

Poliwrath: Water/Fighting
Politoed: Water

Glalie: Ice
Froslass: Ice/Ghost

Solgaleo: Psychic/Steel
Lunala: Psychic/Ghost

Version counterparts:

Cranidos/Rampardos: Rock
Shieldon/Bastiodon: Rock/Steel

Tornadus: Flying
Thundurus: Electric/Flying

Skrelp/Dragalge: Poison/Water or Poison/Dragon
Clauncher/Clawitzer: Water

Xerneas: Fairy
Yveltal: Dark/Flying

Houndour/Houndoom: Dark/Fire
Electrike/Manectric: Electric
Poochyena/Mightyena: Dark

Heracross: Bug/Fighting
Scyther: Bug/Flying, Scizor: Bug/Steel
Pinsir: Bug(Bug/Flying in Mega)

Mega Mewtwo X: Psychic/Fighting
Mega Mewtwo Y: Psychic

Cottonee/Whimsicott: Grass/Fairy
Petilil/Lilligant: Grass

Purugly/Glameow: Normal
Stunky/Skuntank: Poison/Dark

Mr. Mime/Mime Jr: Psychic/Fairy
Bonsly/Sudowoodo: Rock

Spoink/Grumpig: Psychic
Numel/Camerupt: Fire/Ground

Murkrow/Honchkrow: Dark/Flying
Misdreavus/Mismagius: Ghost

Kakuna/Weedle: Bug/Poison
Metapod/Caterpie: Bug

Spheal/Sealeo: Water/Ice
Seel: Water

Baltoy/Claydol: Ground/Psychic
Gulpin/Swalot: Poison

Horsea/Seadra/Kingdra: Water->Water/Dragon
Krabby/Kingler: Water

Slowpoke/Slowbro: Water/Psychic
Psyduck/Golduck: Water

Alolan Vulpix-Alolan Ninetales: Ice->Ice/Fairy
Alolan Sandshrew-Alolan Sandslash: Ice/Steel

Passimian: Fighting
Oranguru: Normal/Psychic

Turtonator: Fire/Dragon
Drampa: Normal/Dragon

Kartana: Grass/Steel
Celesteela: Steel/Flying

Stakataka: Rock/Steel
Blacephalon: Fire/Ghost

Entei: Fire
Raikou: Electric

Golett: Ground/Ghost
Baltoy: Ground/Psychic

Regigigas: Normal
Heatran: Fire/Steel

Edit (06.05.2018): Added USUM stuff