2014 Rubicon smoking?

Hi I’m new here and I realy do not know much on the mechanical side. I have a 2014 Rubicon that started idling high and smoking like a mosquito fogger. I took it to the shop and after waiting 2 weeks for them to get to it they call today and tell me I have mud in my engine? I’m the only one that has ever driven it and it has never even been close to being submerged. They pulled the manual start rope and it will not retract. I asked him how it could have gotten in there and he told me through the exhaust. I told him no way it never even been close. Then he told me the crankcase has a weep hole on the bottom and the mud could have gotten packed in from there? How the heck could it keep water out if that is the case? He told me the motor and transmission would need replaced. Is this possible or do I need to seek a 2nd opinion? This is the Honda dealership. Oh ya and the oil looks clean. Thanks