Where was the rest of the Factions during the assassinations

They weren't around or aware. You can see in the first movie that everyone lives in different parts of the region. There is little mixing of Factions. As Insurgent showed, Amity is in farm lands. Candor is closer, but their hands are tied, as Erudite controls the information that reaches them. Erudite waged a PR war long before the coup, where many people believed Abnegation was stealing from the other factions, that Abnegation leaders were corrupt and trying to break the faction system. Candor can't act without evidence. And even if they could, it's not their role, as seen in Insurgent. Also, after the coup, which seemed to succeed anyway, they continued to seed false info, blaming rogue dauntless. The Erudite leader got out Scott free.

We have to take into account that A, the coup spanned hours. Less than a day at any account. They didn't have time to react, even if they knew right away. Remember, Erudite was lying to them after the coup so when they found out. And B, Dauntless is the military/police. They have all the guns, training, and killer instinct. A bunch of lawyers and farmers have no chance against them by themselves. Candor has some strength, but even then, Eric men were able to run roughshod over them, putting everyone to sleep and tagging them with the remote control sensors.

It took Dauntless rebels and the faction less to meet the Corrupt Dauntless/Erudite forces head on.

The other factions weren't aware of the assassinations. At one point in the film where Four shows Tris that Erudite were getting in serums very early in the morning. Early in the morning could suggest that Erudite were being very secretive about the whole plan.