Probably a glitch & the game isn't reading the file .. Happened to me today
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Ive seen somebody mention "disappearing mons" on here before. Ive never noticiced anything missing on mine. If you dont have any kids or an evil GF then a possibility is pocket poke delete which is like pocket dialing but instead of dialing you delete a mon.
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It happened to me today, too. I would think it was a "pocket delete" like Top Dog says, but I noticed it right away, and I had my phone in my hand the whole time. I also think it's a bit difficult for an inadvertent delete, since it would have to accidentally hit the right spot twice...
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Does it show up in your Journal? And if so, do you know how many candies you had before and how many candies you have now?
This would tell you whether you inadvertently discarded it...
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i never saw that happen, although i was watching a video from a guy in brazil whose a wild nidoqueen has fled but his internet bugged and when he checked his mons the nidoqueen was there.
jump to 17:01
https://www.youtube.com/watch?v=vL7YMastOkM