Kaphotics

Use the database tool. Clear boxes, load pkms, open database, click the filters from the top left dropdowns.

you saved your game and restored an old backup. delete the secure value or use a different homebrew app like svdt or jksv

One of the comboboxes (dropdowns) was filled out incorrectly. Please be sure you spelled the Pokémon species name right.

Feel free to not use it.

Compile the latest commit to pk3DS, it has text randomization.

https://github.com/kwsch/PKHeX/issues/192 Next release.

Implemented in latest commit, thanks for reporting Deals with the ability[1]=0 issue as well as the PID not updating for a selected ability.

You can't catch Regigigas at "Poké Transfer Lab". If the pkm is from gen4, The "Game" needs to be D/P/Pt.

What's New? - Added: Gen III, IV, V Save Editing; Batch (Mass) Editor - Improvements & Fixes: Oodles. 8/22/16 - New Update - Added: FBI homebrew save file detection. Thanks poutros! - Fixed: Program now indicates the type of blank save file loaded if none is detected on startup. - Fixed: Vivillon form Showdown Import behavior. Thansk sora10pls! - Fixed: Vivillon form selection in Trainer Editor re-enabled. Thanks Tsunamical! - Fixed: Program should now load data much quicker; includes save files, box slots, and pcdata. - Fixed: Past gen transfer / save file bugs. Thanks vacero, JSS, Ninjistix & Porta_14 - Fixed: Mystery Gift manipulation now behaves better. Thanks jonaththejonath, sora10pls, Odaxis & rush2802! - Fixed: Legality indication persists when loading a save file. - Fixed: Hyperspace Fury legality. Thanks RanEncounter! - Changed: Batch Editor improvements for PID/EC writing. Thanks JSS & Pokegeo! - Changed: Updated Spanish and Chinese translation. Thanks ajtudela & easyworld!

Most of the time it's a check from the egg creation code, as a special case for the species ID. http://www.smogon.com/forums/threads/past-gen-rng-research.61090/page-38#post-4306581

Pokémon can only be injected to save files; there is no GTS exploit that allows for single Pokémon to be injected. The initial save loaded when the program starts has been changed to Alpha Sapphire instead of X/Y; new release will be posted in a few hours.

PKHeX loads a default X/Y save file when the program starts. Load your save file.

Explains this tweet: https://twitter.com/MrNbaYoh/status/766756928127168513

PKHeX is a computer program, and has nothing to do with the 3DS. You need a way to retrieve your save file from your game; once you do that you can edit the save file with a save editor (ie PKHeX). From the stickied download thread: PKXs and edited SAVs CAN be injected into your game ONLY IF you possess either: Homebrew Menu & Save Manager App X-20 thru X-22 Applet Version (the number after your Firmware Version, no new3DS) using Web Injection <=9.2.0 Firmware Console using SaveDataFiler JP Cart+JP System using Cyber Save Editor & Dongle

PKHeX has a legality checker built in for gen6 Pokémon.

Did you modify any CRO's?

Did you refresh the view of Windows Explorer? It doesn't automatically update unless you refresh or inspect properties. Try deleting the original garc too.

Fixed in latest commit, thanks for reporting

It puts the GARC in the same folder as the source; check date modified.

Should really install homebrew to edit your actual save file. Fixed in latest commit. Thanks for reporting!

Fixed in latest commit. Thanks for reporting!

Fixed in latest commit. Thanks for reporting!

No, PKHeX will only support official games.

Again, Use pk3DS's GARC extractor, not any of those tools from outdated guides. Do not use GARCTool, only use pk3DS. pk3DS properly extracts multilanguage GARC files.

Use pk3DS's GARC extractor, not any of those tools from outdated guides.