PKHex's legality checker isn't 100% accurate. If you upload your Pokémon here, I can take a look at them. You could also try battling with one of your Pokémon at a time until you find the one (or more) that are causing the problem.

 

Battle at what time and where?

— Posts automatically merged - Please don't double post! —

Nope, I never named them

 

Okay, I will try this and then tell but is this the problem because I made the Pokemon through PkHex Mac version? Even though this version tells if a Pokemon is legal like PC version.

My Pokemon:
Zygarde 50%@Sitrus Berry
IV spread : All 31
EV spread : 252 HP , 78 Def , 180 Sp.Def
Ball : Beast Ball
LV : 100
No nickname
OT : Sun
ID No. : 603510
Ability : Power Construct
Moves :
-Toxic
-Protect
-Rest
-Sleep Talk
No relearn moves
Nature : Careful
Date met : 11/26/2016
Level Met : Lv.50
Origin game : Sun
Met location : Route 16 (not fateful encounter nor found as egg)
Language : English
Country : United States
Sub region(set) : Texas
3DS region : Americas

(Shiny) Mewtwo@Mewtwonite X
IV spread : All 31
EV spread : Att 252, Def 20, Sp.Def 20, Spe 218
Ball : Poke ball
LV : 100
No nickname
OT : ASH
ID No. : 56708
Ability : Unnerve
Moves :
-Ice punch
-Earthquake
-Drain Punch
-Bulk Up
No relearn moves
Nature : Jolly
Date met : 1 /24/2017
Level Met : 70
Origin game : Red
Met location : the Kanto region (not fateful encounter nor found as egg)
Language : English
Country : United States
Sub region(set) : Texas
3DS region : Americas

(Shiny) Darkrai@(no item yet)
IV spread : All 31
EV spread : 6 HP, 252 Sp.Att, 252 Spe
Ball : Poke ball
LV : 100
No nickname
OT : RyGuy69
ID No. : 08675
Ability : Bad Dreams
Moves :
-Dark Void
-Dark Pulse
-Ice Beam
-Dream Eater
No relearn moves
Nature : Timid
Date met : 1 /25/2017
Level Met : 100
Origin game : Platinum
Met location : Poke Transfer
Language : English
Country : United States
Sub region(set) : Texas
3DS region : Americas

(Shiny) Zekrom@(no item yet)
IV spread : All 31
EV spread : 252 Att, 6 Sp.Def, 252 Spe
Ball : Ultra ball
LV : 100
No nickname
OT : Ash
ID No. : 25489
Ability : Teravolt
Moves :
-Dragon Claw
-Hone Claws
-Fusion Bolt
-Bolt Strike
No relearn moves
Nature : Jolly
Date met : 11/23/2014
Level Met : 50
Origin game : Alpha Sapphire
Met location : Fabled Cave
Language : Espanol
Country : Mexico
Sub region(set) : Veracruz-Llave
3DS region : Americas

(Shiny) Arceus@(no item yet)
IV spread : All 31
EV spread : 6 Att, 252 Att, 252 Spe
Ball : Cherish ball
LV : 100
No nickname
OT : (Japanese)
ID No. : 03075
Ability : Multitype
Moves :
-Dragon Claw
-Earthquake
-Swords Dance
-Extreme Speed
No relearn moves
Nature : Jolly
Date met : 3 /7 /2015
Level Met : 100
Origin game : Alpha Sapphire
Met location : Pokemon Movie 15
Language : English
Country : Japan
Sub region(set) : Chiba
3DS region : Japan

(Shiny) Kyogre@blue Orb
IV spread : All 31
EV spread : 6 Def, 252 Sp.Att, 252 Spe
Ball : Master ball
LV : 100
No nickname
OT : Ｋａｚｏ
ID No. : 02016
Ability : Drizzle
Moves :
-Ice Beam
-Thunderbolt
-Surf
-Origin Pulse
No relearn moves
Nature : Timid
Date met : 6 /11/2017
Level Met : 50
Origin game : HeartGold
Met location : Poke Transfer
Language : English
Country : United States
Sub region(set) : California
3DS region : Americas

 

I edited my message above, please take a look at my pokemon information.

 

PKHeX is not always entirely correct, for example, while Hypnosis shows in the green-list for Gardevoir, (everyone knows Hypnosis is legal for Gardevoir) If I give Gardevoir hypnosis, it gets flagged a an illegal move.

 

Teach me your ways, Senpai!!!

 

This is true. But PKHeX should have flagged it as illegal.

So I think OP just isn't checking the legality after the edits.

 

Put them in a zip folder?

 

upload it to a file sharing site like filetrip, mega, dropbox etc.
Put it in a .zip

 

PKHex does not flag all of these as legal. You should have checked to see what the errors were and fixed them.

• Mewtwo cannot learn Ice Punch and Drain Punch in Gen I nor Gen VII.
• Kyogre's PID and EC should be the same if it's from Gen IV.
• Rayquaza's OT is from the non-shiny Japanese Gen V event, not the shiny one.
• Darkrai's PID and EC should be the same if it's from Gen IV.
• Arceus is apparently fine.
• Zekrom is apparently fine.
• Zygarde has the wrong Poke Ball.

PKHex isn't always correct.