If you read the issue, SPOILER WARNING: he actually figures out that the Agents aren't really bad guys through detective work and paying attention to his spider-sense. Jimmy Woo is about to confess and tell them about the infiltration plan when M11 apparently recognizes Logan from a mission to Cuba in the late 50s - I don't have that story to hand right now, but it was, you know, a typical flashback!Logan story with a high body count - and attacks without warning. So then all hell breaks loose.
So yeah, he was actually pretty smart! Ten times smarter than he is in his own series, sadly.