It appears that there is a bug about certain links where nutch erases all markers and not only the inject, generate, fetch, parse, update markers but also the distance marker.
The problem is that Nutch Generator doesn't check the validity of the marker distance (check if it's null) and keep wrong links (without the distance marker) in the GeneratorMapper. When the distance filter is activated, GeneratorMapper choose also URL without markers and so it doesn't repect the limit.
I think it's in relation with the problem mention here : NUTCH-1930.
This patch doesn't solved the problem which is all markers are erased (without any reasons apparently ..). But it can allow to stop the crawl...
In order to find a solution about stopping crawl with problematics URL, I proposed this solution which is simply to avoid the URL when the distance marker is NULL.
(Sorry if i put the code here)
Example of link where the problem appears (put an http.content.limit highter than the content-length PDF) :
Hope it can help ...