Does resigning from industry job before probation / 'CV gap' reflect badly in PhD application?
Definitely mention it. Always keep your CV honest and complete. 
I'm unfamiliar with your field; but in the fields I'm familiar with, a fairly casual "Was excited about opportunity, and to gain some industry experience, but my passion is academia" should be enough. A lot of people don't go straight from undergrad to Ph.D. - most of those worked in industry for a while to realize that they'd rather do research. I don't see how when you quit matters. Shouldn't be a biggie. (I'm not commenting on whatever field-specific requirements or conventions you allude to)