Overcharged Ship

Not an anomaly. Side missions. I feel like a fail safe should be put in place for this though. No Captain would knowingly allow a ship to be overcharged to an unsustainable rate. I've accidentally received 5000+. Warp 4 with shields is the only fix

I believe he's referring to the floating anomalies in space that can boost your power.

I think it was an accidental pickup that got them to that state, not willing mission completions.

But the chances of completing multiple energy missions during escort/docking seems much more likely than collecting 3 anomalies upon docking

It can happen as Lucas says. You dock at a station circled by enough allies and far enough in to an invasion and you can end up getting a huge boost to energy, shields, weapons... it all depends on what missions have come through. In the case above, it is obvious that there had been a lot of missions for energy that were overlooked by the comms officer, or just left because it is too much of a detour. Head to the base with the allies and you get all the missions completed in one. It is rare that it happens. but it does and I have witnessed it myself, just not to such a serious extent.

Above a certain level of energy, your ship begins to sustain damage due to the massive amount of power in the system. I believe it was added to stop player collecting all the anomalies on tha map in one go.

I completely agree with the sustained damage from the overcharge, I just feel a failsafe should be put in place to prevent sub-missions to be the cause of the overcharge. Allowing a final acceptance protocol for the mission supplies would be one method.