I think I got the Magnemite due to me playing Hardcore so it was even more difficult to begin with. I havent had any glitches or anything like that so thats rough for you ma dude. best be is to join there discord and ask them. I havent had any problems with Shedninja or saves. I'm not sure what...
You should of got the Nincada unless you dont have the latest patch.
General walkthrough of my team to make it easier for you to get a general idea of what I did.
Taze's Luxio
Onyx - Stealth rock set up, usually survives one hit and can use a Rocktomb on luxio
Hitmonlee - Double kick Luxio...
I think that's the good part of the gyms. If they followed traditional maingame tactics of not having counters to there team it would be boring. This isn't the first time trainers have had other type pokemon to counter their weakness. If you reference back to the anime with Ash ketchum Pokemon...