If the filter is dirty...need to change it.
Also why type of fuel are you using? Bio? DSL? or a mix like B20? Sounds to me like ur tank lining finally let go and ur filter is catching it.
The filter shouldnt let anything but fuel past it so I wouldnt be worried about a chunk of somthing getting into the injectors but if theres that much crap in the bottom of the fuel bowl u need to keep cleaning it out. Try ebay for better prices on a lot of 5 or so filters for $50 I know napa charges $40 just for one!
Just be sure u drain the bowl before you take the filter out....if done it a few times cuz i fergot and what a mess!
Filter wise...if its black when it should be tan it means it dirty.