I initially wrote the parser for a (proprietary) query language compiler using LPEG, and keeping track of lexical issues (whitespace, etc.) along with the grammatical structure complicated things. When I broke it apart and wrote a quick FSM-based lexer and a recursive descent parser, it became much simpler. Perhaps I could have factored the PEG grammar better, but with every PEG grammar I've had grow beyond a certain point, I've wished I could separate the lexing and parsing stages.

I much prefer working with LPEG to regular expressions for small to midsized stuff, though.