I just reread Civil War #5, and in reality, the ONLY inconsistency I can see of (in regards to Spidey), is when he encounters that little exploding toy. His Spider-Sense should have warned him ahead of time, but let's face it... his Spider-Sense has NEVER been able to tell him WHAT the danger is... just that danger is emminent. It's quite possible that his Spider-Sense was already off the charts being pursued by SHIELD agents in the sewers (not to mention the gators

).... and the explosion was big enough that even if he did have time to jump out of the way, where was he going to jump? He was blown through the wall. He could have webbed the little toy up, but it appears to have really caught him off guard (yet another stab against his Spider-Sense, but I have to believe it was already off the charts).
And even a stunned Peter Parker (it really was a big explosion) can get caught in some hallucinagen gas by Madd Jack (we've seen Peter suck up gas before from other villainous pumpkin throwers), and it's more credible that theu can get the upper hand once he's gassed.
It's the Spider-Sense/toy bomb thing that bothers me the most, but what's done is done.
I hope the rest of the story can kick into higher gear.