Helloooooo... IT'S A WAR!
People get killed in war. Some get taken prisoner by the enemy. The enemy doesn't necessarily play by our rules or follow our game plan. "Stuff" happens. It's to be expected.
Some of the Chicken-littles were, for some reason, expecting a cake walk. If things were going to be that easy, Bush would have sent Rumsfeld by himself armed with a baseball bat. No one expected this to be easy. Fast, perhaps, but not easy. Why? Because a considerable chunk of the Iraqi population have hitched their fortunes to Saddam's. If he goes, they're ruined. They've made their way in the world by torturing and oppressing their countrymen. They could find their necks stretched when this is over and thus have nothing to lose by fighting.
However, they will be overcome.
The stiff resistance in places like Basra and Umm Qasr are being led by Iraq's societal elites. They are, ironically, the most westernized group in Iraq. This is why they're able to function without command and control from Baghdad. But the troops fighting under them are not so westernized. They don't do well on their own; they need to be told what to do and when. When the Special Republican Guard and other Baathist elements in these pockets of resistance are taken out or their communications disrupted, the resistance will falter. The troops under them cannot function independently at those moments and are vulnerable.
These stories of Iraqi resistance aren't worth all the running around and screaming that some are doing.