It is normal in all cave diving to have a line. If I remember correctly, it is not necessary to run one's own primary line into the cenote where he entered, because the permanent line comes out to open water. (This is not a tourist cenote; there is no cavern zone to speak of, and no open water to snorkel in.) There are many possible branch lines one can take, and it is customary to tie a spool into the line you are on, and run it to the line you are going to go off on, and mark the exit direction on your original line, so that when you come out, you can't get confused. Sometimes, when the distances are short, people don't run a line -- that's called doing a "visual jump".
Whether that played any role in this accident or not, we will almost certainly never know, because if the diver DID run lines, he would have collected them on his way out. But it is one way that you can get lost. You can also get lost by swimming onto a side line by accident, because you didn't see that your own line went a different way. You can get lost if you silt something out to where you can't see and have to search for the line, or because the line gets broken. There are a lot of ways to get lost, especially in very spiderweb-like cave like Calimba.