Well, Hence many Jedis got away from what we know it. And in defence of Secura, She did notice something is wrong, but is distracted by other things. People like A'Sharad Hett escaped in other ways also. And, many of those Jedis would escape the initial clone attack to be hunted down later. Some would just decide to live like non jedis.
Btw, to the clones this is just an order like always, with no special emotion attached to it, making it much harder to sense, especially when jedis do not usually like to peek into others mind.