Originally Posted by StrainedEyes
Eli noticed that Knox's initials on his handkerchief were JMT, which obviously don't match the "Warren Knox" name that the agent has been going by.
It should be clear to Eli that things aren't on the level with Knox. He's not that thick-headed not to notice, I don't think.
Now the question becomes what does Eli do with that information. I wouldn't put it above Eli to try and betray his brother again.