These would probably count as "annoying" bugs.
(1) When I compile a Lilypond file that contains an error, Lilypond
should not open up the previous .pdf file: An error means I have to go
back to the file, which means closing the .pdf file first. (This could
be added in the form of a preferences menu with items like "behavior
upon error" and "behavior upon warning". Default would be "compile and
open output file".)
(2) When I compile a Lilypond file, make some changes, compile it
again, and so on, the various compilations in the log file are
continuous. Some sort of a separator (even if it's just hyphens)
should be put between compilings.
--- Christopher Heckman