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The top may need recalibrated......have seen that a few times.
There is a hall type sensor in the clam shell motor which usually doesn't go bad, what can keep it from shutting is the ear flaps that flip up after the top is down.....there are micro switches for those, if they aren't working then that is the problem.

You can get to the connector for both flaps by pulling the rear carpet piece that is under the clamshell, they are attached to the rear section just behind the roll over bars.

I have seen where the flaps get stuck and you can manually turn the threaded Rod which they ride on with a torx bit, which you can see by looking strait down next to the roll over bar cover, there may be a cover on them....
See if the flaps are moving first...