I'd get in the loft and check that they have actually supplied a fan with timer and that their real problem isn't that they've fitted the wrong fan. If the cabling is accessible then the wiring they're talking about only involves a bit of 3+E cable. Be a bit odd for them to fit a fan + timer and not wire it for the timer to work.
If you haven't paid him I wouldn't until it's fixed. If they've fitted the wrong fan then you know that they've lied to you.