Hi folks. One common source of confusion with Inoculators is the difference between "Uses" and "Charges". Each time you activate the inoculator, it expends some amount of charges. The amount depends on the inoculator components you have selected. The psychon component adds +3 to the charge cost of a single inoculator use. Having two adds +6. The total cost can be seen when configuring the inoculator, just under the syringe icon.

Medical supply boxes drop two 4-charge items, for a total of 8 charges. If you are using a configuration that has a high cost (for instance, 3 psychons, which costs 9 charges), then a medical supply box will give you the 8 charges, but that can still be insufficient to provide you with another use (meaning a red dot will not fill up on the game UI). This also depends on your total capacity, since "uses" are rounded down in the game UI while playing, but you still have the same total capacity behind the scenes.

I don't know that this is the situation you are in. I re-configured my own inoculator to 2-psychon/2-purifier (a total of 6 charges per use), and verified that medical supply box does indeed recharge my inoculator, so the psychon component is not bugged, at least not in all cases.

Can one or both of you verify that the problem you're seeing is not related to the fixed number of charges that a medical supply box provides?

It happens with three psychon as well. It happens every mission, so it is pretty repeatable. Simply ask if you would need more information.