When Morpheus takes most of his crew into the Matrix to take Neo to the Oracle, Tank is watching them. His job, at that point, is to watch out for them and look at what's going on around them.
When Cypher walks out of the building and drops his cell phone, still on, into a trash can, nobody on the crew who is in the Matrix can see him, but why wouldn't it be clear to Tank what he's doing (since Tank would be watching the code)? And wouldn't Cypher be aware of that as a possibility? He would know that Tank was watching them, so even if those inside the Matrix didn't see it, he should know there's a good chance Tank could see it.