Such confusion - spoilers....
I read a couple of pieces about this movie and one where he commented on the title - that reptiles shed their skin and become anew, or something like that - that people change.
And here is where some of my confusion lies what was the purpose of the shed snake skin in the house by the window? Also, what did the wax peel of Benicio's hand represent? Made no sense to me.
Also, at one point (I think it was during the dinner scene later in the movie), Benicio's wife looks at him as if she knew of the corruption that was going on and may have even been a part of it - which only added to the confusion of the wax peel of Benicio's hand - it made me think he was also shedding skin but who knows into what.
I get the use of red herrings, but to merely use them apparently to only confuse an audience to a complete fog isn't a good use of them, IMHO. In uses like this, it seem to be done more out of lazy writing than creative writing.