A slab repair or something bigger?
In our bathroom vanity cabinet, you can see the pipes going straight into the ground. The tile was never finished out around the pipes. Lately after it rains, our bathroom smells very musty (btw, this is on the first floor). Could this solution be simply to seal the hole or could there be another greater issue?
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Brandy,
Can you see dirt around the pipes, or a concrete slab?
If you can see a substantial amount of dirt, the first step would be to cover the dirt with a carefully shaped piece of polyethylene, and then to pour a small amount of concrete on top of the polyethylene. (You can buy a bag of Sakrete and mix the concrete yourself.)
Then you would need to caulk around the pipes after the concrete has cured.
If you can't see dirt -- just concrete -- then you should seal around the pipes with canned spray foam or caulk.
Try these remedies and see if these help reduce the smell. In the meantime, don't forget to use your bathroom exhaust fan when you use the bathroom.
It's certainly possible that your bathroom floor has other problems, but it's hard to know until you at least try these steps.