On the command line, fill_buffer/1 waits for a terminating newline:

?- sleep(4),fill_buffer(user_input).
hello|: hello
true.

The `hello\n` is then hanging in the input buffer and is read by the toplevel on the next occasion:

?- ls.
ERROR: Syntax error: Operator expected
ERROR: hello
ERROR: ** here **
ERROR:
ls .

To consume the data in the input buffer, use read_pending_codes/3:

Here a newline is needed to push data into the stream:

?- sleep(4),(fill_buffer(user_input),read_pending_codes(user_input,Codes,Tail)).
hello world
|: hello world
Codes = [104,101,108,108,111,32,119,111,114,108,100,10|Tail].

But if you read "raw" you don't need a final newline, although the goal still blocks if there is no input (how to make it return at once?)

?- sleep(4),with_tty_raw((fill_buffer(user_input),read_pending_codes(user_input,Codes,Tail))).
hello world
Codes = [104,101,108,108,111,32,119,111,114,108,100|Tail].