for the charged quarks issue i have not encountered it so the progress bar for it is full have you purchased the upgrade that unlocks it that might be why and for increasing energy values the reason is cause they are gained through an mechanic of charged quarks which is why you are unable to gain energy and about the mobile i will try to work on it as its mostly designed and expected to be played on Pc but i will see what i can do
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I've yet to try it on desktop so perhaps I just hit a limit caused by mobile incompatibility? So not technically a bug as its not designed to work on a mobile...."working as designed". I believe I'd bought the upgrade that should have activated Charged Quarks as I was certainly buying upgrades that were meant to improve CQ output which I presume would come after.
Erm, I may have just found a genuine bug! So I was playing last night on my laptop from scratch. Reached my first SA reset and logged off not long after. Today I've opened the game and the SA and Automation tab has gone and Particles are no longer generating despite me having plenty of Quarks to be generating them. I also still have the SA achievement so the game does "know" I've got that far.
Tried closing and re-opening the game, but no change.