I dunno. I've probably never learned a song 100% if you include every note-for-note nuance, but I'm not sure if that's so important. I mean, maybe it is if you're in a tribute band, but otherwise not so much.
But to your point, yes I can relate. I focus mainly on one little blurb at a time.
However, if it's a song I either really like or want/need to learn, I will go through it until I get stuck, and then isolate that one part. I'll then make sure I understand what notes I'm supposed to play (using a variety of methods -- ear transcription, guitar pro, tab, videos, etc.) and then just mindlessly practice it whenever I grab a guitar. I've actually made some decent progress that way.
Reading some of the earlier posts just now, I will also reinforce one thing that was already mentioned: when I started playing with other people, it placed a real priority on learning all parts of a song. If a song was too difficult, I'd find some easy workaround until I could play it the right way, but the accountability of playing with people was probably the best way to bring my playing into focus.