Yeah this mechanic is totally unfair I lost like an hour of my progress :(
Viewing post in what do you do when the battery runs out?
If you are playing on Hard Mode with the challenge statues, you are taking too long to the sweep the rooms. As a general rule, you need to herd the ghosts, and siphon them in groups. You also have to speed up your whitling down of their health for consumption.
Fun fact: I'm pretty sure this comes from old arcade games where running out of time kills you. So you have to understand the game well enough to play it properly.