Your statements and questions are confusing to an electrical engineer. Do some reading on voltage. It is a force (electro motive force). Do some reading on charge. It is associated with the flow of electrons and current.
Let me reword your first stated observation as I understand it:
1) After discharging a battery (current flowing) for 1 hour, you measured the ending voltage and compared it to the starting voltage.
Under what conditions did you measure the voltage? Was the battery supplying current to the light (aka "load")? If so, then this would be the "starting and ending load voltage"? Was the battery disconnected so you measured the open-circuit voltage? Were the "loading" conditions different between the starting and ending measurements? If they were under different load conditions, then you can't compare them scientifically because you don't have sufficient data to characterize the operating condition. Voltage alone is insufficient to characterize the state of a circuit.
I'm horribly confused by the statement
start charge of hour 3 was greater than end charge of hour 2
when I reword it assuming you meant voltage:
starting voltage at the beginning of hour 3 was greater than ending voltage of hour 2. This can't be unless there was a time and condition difference between the ending of hour 2 and the beginning of of hour 3.
If I assume that you measured the ending voltage of hour 2 before you measured the beginning voltage for hour 3, then there was time for the internal battery state to change. For the voltage to go up, then I have to assume that you were measuring the open circuit voltage at least for the beginning of hour 3.
Forgetting your incompletely specified observations, let me describe what can happen in a battery discharge and recovery cycle:
When you put a constant load on a battery, the battery supplies a current flow and undergoes internal chemical changes for this to occur. There are physical distances involved between the annode and cathode materials and there are surface areas of the annode and cathode materials that form some electrolyte geometry. During current flow, there is dispersion of ions, electrons, and semi-reversable and irreversable chemical reactions going on in this geometry. When the external current is distrupted (load disconnected), the state of this electrolyte geometry and any reversable chemical reactions at the annode and cathode can redistribute and the electrolyte space will undergo a balancing dispersion of ions. If you measured the voltage during this rebalancing, it would likely increase as the electrolyte state balances itself out.
Look up dispersion for a better understanding of it. To get a visualization of it, you could drop a drop of food coloring into a clear glass of water and see how the color spreads out with time. The initial drop falling into the water proves some initial movement.
In the case of the electrolye ion rebalancing, some imbalanced force exists that is being used to rearrange the ions until they are balanced. The force being used to redistribute the ions somehow takes away from the electromotive force seen between the annode and cathode (voltage).