Not that this is game breaking, but I leveled up my allys on an alt today. got oracles to lvl 3, thru her on passive and then went to fortify my calculator bot and tried to select 2,000 of my favor, but everytime the gear repair sound went off the amounts were hidden in the background, unable for me to click accept or do anything else to it. simple solution was to either unequip oracles or what i did and that was let her get all my gear to 100. but still, weird and figured i would post it for ya's i did not troubleshoot and see if it happens to regular inventory stacking, i only tried the ally favor again and again hoping i could be fast enough....but i wasnt good luck!
This happens to me, too, and it took me a while to realize it was Oracle. But, yeah, if Oracle is doing a repair, each time it happens, I lose my place in inventory. It's happened in the regular inventory, the fortify menu for artifacts / augments, and in the augment selection tab. Like you said, once the gear's full up, it doesn't seem to be a problem, but if I've had Oracle out of her passive slot and just popped her back in to do repairs, I usually have to wait a minute or two before I do anything else inventory-wise.
