Hello both of you,
there is an easy fix to avoid anything like that (at least that's what I always do since this happened to me as well), go and talk to NPC that heals your pokemon in the PC before you start a PVP match, also swap Slot1 and Slot2 back and forth before starting a PVP. :)
thanks Prehax a guild mate told me this also and i have been doing it since. still a frustrating bug that should be addressed and fixed.