I'm still not entirely sure what specifically you're asking about, but I have a guess. It is true that positively-charged hydrogen ions, or bare protons, are typically only observed in gaseous/plasma states and hard vacuums, and it is also true that cells routinely pump positively-charged hydrogen ions across membranes. This is not a paradox because in aqueous solutions, hydrogen ions exist as $H_3O^+$, also known as hydronium or hydroxonium.
![Hydronium](
Image from Wikimedia Commons