That because it's a Call key, not a Line key. Call 1 is not linked to Line 1. It just happens to be the first call processed on that phone. The next call would be on Call 2, regardless of the actual line in use.

For Call keys, you need to use individual hold instead of system hold. Calls need to be transferred or use reverse transfer to retrieve a holding call. It's a training issue.

How many lines do you have in the system?