The basic resource rooms can provide resource in excess of what the capacity actually allows. This results in a situation where you can fill the bar up to full every time you harvest resources, but before the next time you get resources the bar drops below the position of the needed resources gauge. Then when time comes to harvest again, you are back up to full.

Upgrading a room helps with this, but also comes with it's own drawbacks, in that the room events that happen are stronger and harder to deal with. In fact the benefits was what made me upgrade all of my rooms to level 3 to begin with to not have to deal with that situation, instead forcing me to deal with a spiraling catastrophe that I could not deal with.

Rather than making the rooms hold 50/75/100 each, could you increase the capacity of the lower level rooms a bit? Perhaps situating it at 70/85/100 would work better with the current model. Either that or allow combining rooms into bigger rooms also increase the overall capacity by 25% like it does the production.