Hi Jasper @Jasper_Sluis! Welcome to the littleBits forum.
I am not completely sure I understand your circuit, but here's what I think:
You are using an IR beam from the ir led on one littleBits circuit to shine through a (is it a clear bucket? it would have to be, right?) container, to a remote trigger (a remote trigger is an IR detector) in a second circuit on the other side.
When the bucket is full, the IR beam does not make it through and does not 'light up' the remote trigger.
When the bucket is empty, the IR beam goes through the bucket, activates the remote trigger, and the long led turns on (as does the cloudbit, but I'll leave that out to simplify.)
Your problem is that the system does not turn off when the bucket is refilled, right?
If that is the case, try to isolate the problem. Try experiment #1: Cover the remote trigger with your hand. Does the long led stay on? If it does, then the problem lies with the second circuit. Put a timeout between the remote trigger and the long led, and see if that fixes it. Set the timeout for it's shortest duration, and on -> off mode.
If the long led turned off when you covered the remote trigger, try experiment #2: cover the ir led with your hand. Does the long led turn off? If not, then there is a source of infrared other than your ir led. Put some sort of light baffle around the remote trigger. Perhaps a shade would do, or maybe you'll need a cardboard tube that is painted black inside.
@alexpikkert, have you any ideas?