I remember hearing the ticking but I paid no mind to it in all honesty. Thought it was just relevant to the room they were in. I don't have a super theory but my guess is its counting down to someones death.

Not sure why but my feeling is CJ. She might do her best to work with Saul and get him to his love lizzy. Sacrifice herself in the process to ensure that Saul gets to her or maybe gets out of the Colony safely with her.