Clogged dies are very common. Typically metal from thousands of planchets have little bits of metal scraped from them when they are struck and those particles fill in the crevices of the die.
But I believe you have die chips and not clogged dies. Clogged dies would not show any mint mark at all or would show only a partial mint mark. Chips happen because the area inside the mint mark is a weak point in the die. The mint mark is hubbed (cut into) the die. You could say that the inside of the mint mark does not have any metal around it to "brace it" from the shock of striking, so they break off leaving a hole in that spot which will transfer as a raised spot on the coin. At least that's how it looks to me. Chips are very common though. Remember dies are backwards from coins. What's raised on a coin is recessed in the dies.
Lincoln cents struck in the 50's used to have chips in the R of Liberty Especially the lower part of the R and they were called a "Skirted R." . Sometimes just half the of the bottom part of the R would be chipped and it was called a Mini-Skirt.
Thank you very much longnine009
So, to summerize what you said
The error name is filled mint mark "D"
The cause is die chips
This error is common and does not increase the value of the coin
Thank you again, you have answered all my questions
