I will try to help, if you mean the tutorial section (where the anomaly first appears) then you need to switch to special weapon by pressing the "3" button on keyboard and only then with the special weapon selected you can use mouse right-click on the anomaly, aim a little down where it's placed on the ground.
If you mean the broken electricity box in the Chapter 1, you can't pick it up, since it's constant electricity from the city's power line and your anomaly manipulator only works on anomalies. You need to find switch to turn off the electricity.
I checked it and I was not able to recreate the bug where the anomaly manipulator did not work, it works consistently for me, perhabs the screenshots will help you though, let me know if it worked now.