If I remember correctly, what he meant was this: There was a redundant charge that never went off. Only one charge would be needed, higher up on the lines where they converged close together. This charge would blow all of them.

What this was supposed to look like was a mistake. That "Jason Bourne" had left a second explosive that malfunctioned, which left his finger print behind. Danny Zorn essentially knew right away that something about this setup made no sense. Bourne would know that only one charge was needed, a charge higher up on the lines where they converged (instead of two charges lower down). So to Danny Zorn, this felt like the frame job that it was.

What was Zorn referring to by, "Why put the charge all the way down here?" Did he mean "why put the charge in the breaker room rather than somewhere else in the building?" If so, where would a better spot have been?

Observation #1

The office building's electrical closet was located in the basement, and the entrance to it was in a back/side alley.

When Kirill is first shown going to the electrical closet to plant the charges, we see that he turns into an alley and enters through a door that's at ground level. After traveling down at least one flight of stairs, he reaches the end of the stairwell (the lights are off), and enters the electrical closet.

Kirill accessing the electrical closet through a back/side alley.

Additionally, when Danny leads Abbott to the closet, it shows the same thing.

Danny Zorn leading Ward Abbott to the bottom of a stairwell, where the electrical closet is located.

Observation #2

The Neski files deal took place on the 3rd floor.

Top left - lights are on; top left - lights are off; bottom - office building with ground in frame.

So, with this in mind, what Danny meant was..

If the person who blew the power and hijacked the deal is obviously highly skilled/trained, why would they go through the extra hassle of creating the explosives and going all the way down here [to the basement] to plant them, just to have the lights off?

Saying what he did, Danny was simply emphasizing the distance from the office where the deal took place (3rd floor), and the electrical closet that's all the way outside, around the back/side of the building, and down some stairs in the basement.

Danny's other point

The charge that did successfully detonate was attached to the main riser, which is the power line that runs up the entire building and provides electricity to each floor. Consider the following image of a typical building layout:

Primary power source is located at bottom most floor and spans the entire building via riser.

Clearly, if someone is knowledgeable enough to create and plant plastic explosives, and are able to identify essential power lines, they would also know that the line going to the sub-panel on the floor just above is pointless to target, and they wouldn't have planned for such a thing.