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is it possible for mud to cover the pea gravel so it would not drain into the sub pump.?
Yes, but it's more likely the mud will clog your pump before it ever stops the drainage to it.
There are many types of "sub" and "sump" pumps but they all require a higher volume of fluid to debris to remain operable.
Is it possible for clay, mud, silt, to clog up a drainage system? you betcha! Is it possible to cap off a pea gravel area with clay/mud and prevent perking to the earth below, or make the area less permable? Yes Siree!
Its also possible for drain tile to collapse/break.
So yes, James it is possible your drainage system is choked and it could very well be preventing drainage to your sump pit.