Here is how to fix ore cleaning in OSRS.
First, check if you're depositing pay-dirt correctly. The hopper needs your pay-dirt to start the cleaning process. Put your pay-dirt into the hopper connected to the water circuit. Your cleaned ores will then flow into the sack for collection.
Did you log out or leave the mine with ores waiting to be collected? Don't worry - they should still be there when you return. The game saves this information when you log back in.
For missing golden nuggets, try this trick: deposit only half of your pay-dirt at one time. Drop the other half on the ground first, then deposit. This prevents nuggets from disappearing, which is a known bug some players face.
If you're using the Blast Furnace instead, you might notice it not taking your full ore inventory. This happens when leftover coal or bars get stuck in the furnace. Before continuing, make sure you remove all bars from the collection area. You might also need to use up all remaining coal before adding new materials.
Want to maximize your mining efficiency? You might need more gold for better equipment. You can buy OSRS gold to upgrade your gear faster and make the ore cleaning process smoother.
After mining sessions, I like to relax at my house in Hosidius. If you're new to the area, check out this guide on how to enter Hosidius house in OSRS for a useful mining break location.