Probably because he was bowling like a D grade club bowler at that time. Bowled consistently too short in that series, and was still struggling majorly with his action, trying to change it in the nets and bowling naturally in the middle. Not surprising that he struggled really, especially considering he was playing against a top class batting line-up.
As for the Chris Martin issue, it's what fast bowlers do, they like roughing eachother up. Dale Steyn wasn't trying to get Anderson out last summer when he hit him in the head and on the body in a Test match last year, yet I don't see people moaning about that.......
Except there is a difference, Martin can't bat at all. It was a disgrace because I don't think he pitched one ball up for entire over (I'll check cricinfo) but I just remember Crowe saying it was such a cowardly thing to do. Plus he had been bowling rubbish all day irrc.
Plus New Zealand was something like 200 runs behind with one wicket left, why not just pitch it up.