Because Peter doesn't want to kill or excessively hurts others, even bad guys

When you can poke holes in ships hauls with the flick a finger, it's really hard to gauge just exactly how much force you can exert without hurting someone - picture it like those stupid hot water taps in showers that are ice cold -> cold -> cold -> slightly less cold -> burning lava hot.

Peter would have to stay in the cold longer until he adjusts his punches just slightly enough to not reach the burning lava hot

Then add to that that as depicted in Hawkeye, Kingpin is clearly stronger and more resilient than a normal human being. Peter would be used to using just a little bit of force when fighting because he'd be used fighting relatively normal humans, and this time it's not really working because Kingpin can take it, so Peter has to raise his strength: but only one nano-fiber of muscles at a time, because he doesn't know if he were to raise it by two nano-fiber of muscles if it would kill Kingpin or not, but that's enough time for the fight to just look like Kingpin is doing damages - which he's not really doing, just looks like it.

Then there's the clicking element that makes Peter go "yeah ok fuck that" so he takes the risks and raises the temperature just a little bit more than he would have otherwise, and Kingpin gets taken out in a single hit.