I removed a florecent light and wired three can lights on that three way switch. The casings of the cans are really hot. The other lights on single switches are fine. All wiring is okay I am lost.

Mmm..
And the question is? I'll '' assume it's the heat that concerns you. Check the rating of the fixture. Check to see if the mfg. wants it uncovered by insulation. If your installation is proper, and you are using the proper size bulb, then you SHOULD be OK.
But in can lighting, I would recommend cfl's over incandescent.

I agree, I think there is a question in there somewhere.

Missouri is is right on. If everything is installed properly you are fine. Recessed lighting gets hot.

If they are IC rated cans you can ocver them with insulation. If not then NOT!

What brand and model are the cans?