Katrina showed many of the problems with FEMA, though it seems to have improved since then. I'm not sure why enforcement of fisheries conservation belongs under DHS, and as someone who does a good bit of offshore fishing I'm not very happy with they way they over-regulate/enforce on recreational fishermen who would have a hard time making a dent in most populations while (seemingly) turning a blind eye to commercial efforts destroying them.
Others I don't have any insight into, but it seems that DHS has mostly the creation of a huge number of bureaucrats who's major responsibilities involve insuring that the money allotted is spend so that the same or more can be requested for the next fiscal year, with the actual agencies under it getting a smaller piece of the pie and more barriers to actually doing work than before.