Don’t dismiss some physical problem due to the Proxmark3 itself.
Last year, I cloned an Indala 224 onto my xEM (my work badge) and it went silent after I was done. I’m 99.9% certain the reading I did to clone it killed it: the lady in charge of the badges I returned the tag to told me they’d been recycling and rotating the original set of badges for decades as employees get hired and leave the company (yeah, not too smart) and she told me she was amazed and she’d never seen one going tits up. It seemed like an extraordinary coincidence that the only time it should happen was exactly after yours truly Proxmark3-read it.
As far as I know, Indala tags don’t have in-built suicide read counters for sensitive blocks, and there’s no way the PM3 could overpower and fry it. Yet… there ya go. Don’t ask me how, but somehow the PM3 killed that LF tag. I assume it jogged the tag’s circuitry in some odd way that wasn’t expected by the designer and that bricked it.
The same sort of unfortunate command sequence pattern could have weirded out your Mifare too. Highly unlikely, but it’s possible I guess.