For instance, .quit doesn't exit the program when running a script from the command-line (or C's system() ) via .init.
Also, have more than 2 inner joins and a query takes 10 minutes. I fixed this by writing some custom queries.
D. Richard Hipp (the author) refuses to accept these are bugs, when they obviously are. Also, people like Mozilla get first call on bug fixes, so the 'little guy' gets no support for no $$ - I read it costs $75,000 for 'special' status and $1500 a year for support.