Excessive, reflexive use of the pentatonic scale.
Not knowing the names of the notes I was hitting. Learning the fretboard is not something you just do once and you're done -- it's an ongoing process that has to be performed many times over, from many different perspectives. I have been doing a lot of work with fixed-do solfege recently and I cannot imagine ever really "knowing" the fretboard without this tool.
Related: not learning the entire length of the fretboard from day one. My first teacher told me, "there's no money past the seventh fret"; although it might be a sound guideline for playing in an ensemble, it is bad advice for solo playing, practice and overall musicianship. That advice alone set me back a decade or so. I have also been working with the "unitar" concept from Mick Goodrick's "The Advancing Guitarist," which has been really helpful in getting more "horizontal" and "diagonal" perspectives on playing.