it would be nice if they compensated for some of the more major bugs like a mobile game would
Like the thing with magearna is whatever. That seems more of a server side issue, no harm done that we can tell.
Hyper Training def feels like it should have, though at least that seemed to be a more complex bug since the actual pokemon's internals still said "was hypertrained". But still, that's kind of a big deal, at least give some complimentary gold bottle caps.
This is extremely niche (since it involves putting a Nincada in Home, taking it out, then evolving it and putting them back in) but it does result in the deletion of at least one Pokemon in question. Give out a shiny, flawless IV nincada or something as an apology