A few gotchas:
Sometimes user input does not like to work on the first try in Chrome. A few attempts at running the program usually solves that problem, or try this in another browser (firefox works well).
Second, since the looping mechanisms are defined with recursion it's pretty trivial to blow through the stack in JS when running a program with much iteration. These programs should work as expected when using the CLI implementation.
Lastly, user input does not support the line feed character ("\n"), which is a common sentinel value to indicate end-of-input in brainfuck programs. You'll just need to pick some other character.