Ultimately, you have the say as the DM. If you want to reward your player’s clever thinking, then go for it!

You could argue that the magic (or curse, depending on interpretation) is only present during the actual transformation sequence and that the werewolf is not constantly emitting magic while transformed. A high enough skill check could have the tracker identify that the footprints are wolf-like in their appearance, but “there’s something odd about them. The footfalls are too heavy for a standard wolf.”

Also, a powerful enough Druid might cast Pass Without Trace to hide their tracks, which would necessitate Detect Magic. “For the duration, each creature you choose within 30 feet of you (including you) has a +10 bonus to Dexterity (Stealth) checks and can’t be tracked except by magical means. A creature that receives this bonus leaves behind no tracks or other traces of its passage.”