The writers have lost their sanity here.
They used the knife as a reason for Stone going flying--while he could have been defending himself he doesn't get to plead self defense because he kidnapped Stone in the first place--you can kill your kidnapper even if he's a policeman. (Price's actions were not remotely an arrest.)
He's not guilty of shooting Hamilton but the denied medical treatment means Hamilton loses his arm (the tourniquet was on way too long) and Price will go to jail for that.
I have a problem with the chopper finding the initial bad guys--good luck finding a too-warm car during the day, and good luck picking out occupants over the heat of a warm engine. And what's so suspicious about the people being in the van? I've seen plenty of workmen spend a while in their vans looking for a part--and the camera can't say what they're doing inside the van. (Not spotting the guys on the levee is no surprise--all the camera can see is people, not what they're doing. If people are legitimately on the levee there's nothing suspicious.)
There also was no need for the mess. Yes, the red tide could have been an accident--but the fact that NCIS knew about the contamination shows that it most certainly wasn't an accident--and that's enough to show they have a case. Once the situation is exposed there's no way they would have flooded Clearwater. Continuing his plan would be a huge arrow pointing right at him.