From man bash
compgen [option] [word]
Generate possible completion matches for word according to the options, which may be any option accepted by the complete builtin with the exception of -p and -r, and write the matches to the standard output. When using the -F or -C options, the various shell variables set by the programmable completion facilities, while available, will not have useful values.
As this shows, you probably have some variable set to alter the behaviour of the bash completion facilities and the option -F
to compgen
ignores those variables and values, informing you of this with the above warning.
References:
[1] http://linux.die.net/man/1/bash