Here it says
In Lightning Experience, opportunities with products can’t be cloned.
I tested this out and I was actually able to clone and Opportunity with products using the standard clone button in lightning.
How can I prevent this ?
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You can either remove the clone button altogether, or you can create a custom clone button and then put in backend validation in the code to prevent the clone method from inserting the new oppty IF any products are related to the oppty which is being cloned.