Doe's chlorine gas mixture (Bleach & Ammonia) in the lightbulb is an interesting idea, except he should have put the bleach into one bulb and the ammonia into another. Then when he threw them together they would mix and produce chlorine gas. This technique was also used by MacGuyver in the 80's using spray bottles.

The mirror should show a reversed view of the hallway behind Rothman. However, it clearly shows a non-reversed shot of the hallway with the door at the end on the original (right-hand) side.

Why didn't Rothman see himself in the mirror even though he could see Doe standing right behind him?

The terrorist wouldn't have been shocked because he wasn't grounded to anything. Even if he were shocked, he wouldn't have turned "electricity blue." He wouldn't have been immediately knocked out (and stayed out long enough for Doe to gas the other terrorist and tie them together) from only 120 volts. Why would all of this destroy the metal balls?

Doe is shown hurling the shocking device from the ceiling grate. The next shot shows the device wrapping itself neatly around the terrorist's arm. Nice toss.

Doe goes to a lot of trouble to get the meditation balls for his shocking device. It seems that he could have found something as effective, or more effective, somewhere else in the building.

How did Rothman figure out the cameras were active? There's no active light or anything. For that matter, how did John shut down the active light from a distance?

Wouln't Doe have wanted some kind of insulation between himself and a coffee cup containing a mixture that hot? It even appears to be running down his hand in the close up.

The coffee pot apparently has soap in it - shouldn't that interfere with John's chemical drain cleaner/lemon acid mixture?

In one shot we see a black van going down a street. There are white banners on the lamp posts - those are banners promoting Olympic awareness for Vancouver's 2010 Winter Olympic bid - not very likely in Seattle.

At the end it sure looks like Lt. Avery's name plate says "Jame".

Shouldn't Rothman's men have spotted the CDC forces moving in? They report about the area being clear earlier. A better question - why does the CDC come in sirens and lights going?